Starting phenix.real_space_refine on Tue May 14 16:13:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzw_42845/05_2024/8uzw_42845_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzw_42845/05_2024/8uzw_42845.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzw_42845/05_2024/8uzw_42845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzw_42845/05_2024/8uzw_42845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzw_42845/05_2024/8uzw_42845_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzw_42845/05_2024/8uzw_42845_updated.pdb" } resolution = 2.69 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= 0.000 sd= 0.021 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: 5 Type Number sf(0) Gaussians P 10 5.49 5 S 140 5.16 5 C 17742 2.51 5 N 5071 2.21 5 O 5295 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 217": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 310": "OE1" <-> "OE2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B GLU 250": "OE1" <-> "OE2" Residue "B GLU 275": "OE1" <-> "OE2" Residue "C GLU 106": "OE1" <-> "OE2" Residue "C GLU 217": "OE1" <-> "OE2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 275": "OE1" <-> "OE2" Residue "D GLU 349": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E GLU 275": "OE1" <-> "OE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "F GLU 217": "OE1" <-> "OE2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "F GLU 275": "OE1" <-> "OE2" Residue "F GLU 335": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 119": "OE1" <-> "OE2" Residue "G GLU 217": "OE1" <-> "OE2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G GLU 275": "OE1" <-> "OE2" Residue "G GLU 362": "OE1" <-> "OE2" Residue "H GLU 106": "OE1" <-> "OE2" Residue "H GLU 217": "OE1" <-> "OE2" Residue "H GLU 275": "OE1" <-> "OE2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "I GLU 217": "OE1" <-> "OE2" Residue "I GLU 250": "OE1" <-> "OE2" Residue "I GLU 275": "OE1" <-> "OE2" Residue "I GLU 335": "OE1" <-> "OE2" Residue "J GLU 217": "OE1" <-> "OE2" Residue "J GLU 250": "OE1" <-> "OE2" Residue "J GLU 275": "OE1" <-> "OE2" Residue "J GLU 310": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 28258 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2894 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'LLP:plan-2': 1, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2902 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 18, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2884 Classifications: {'peptide': 381} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'LLP:plan-2': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "D" Number of atoms: 2921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2921 Classifications: {'peptide': 383} Link IDs: {'PTRANS': 18, 'TRANS': 364} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2779 Classifications: {'peptide': 365} Link IDs: {'PTRANS': 17, 'TRANS': 347} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2774 Classifications: {'peptide': 364} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 345} Chain breaks: 3 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'LLP:plan-2': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2881 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 344} Chain breaks: 3 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 2737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2737 Classifications: {'peptide': 359} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 16, 'TRANS': 342} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2738 Classifications: {'peptide': 360} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 341} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'LLP:plan-2': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Time building chain proxies: 14.39, per 1000 atoms: 0.51 Number of scatterers: 28258 At special positions: 0 Unit cell: (189.98, 183.372, 81.774, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 140 16.00 P 10 15.00 O 5295 8.00 N 5071 7.00 C 17742 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.34 Conformation dependent library (CDL) restraints added in 5.0 seconds 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6902 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 30 sheets defined 39.7% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.06 Creating SS restraints... Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 102 through 113 Processing helix chain 'A' and resid 132 through 141 Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 186 through 192 Processing helix chain 'A' and resid 208 through 214 removed outlier: 3.682A pdb=" N ALA A 214 " --> pdb=" O ASP A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 251 Processing helix chain 'A' and resid 267 through 270 Processing helix chain 'A' and resid 278 through 284 Processing helix chain 'A' and resid 309 through 316 removed outlier: 3.696A pdb=" N ARG A 314 " --> pdb=" O GLU A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 324 removed outlier: 4.344A pdb=" N ALA A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 removed outlier: 3.520A pdb=" N LEU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 341 " --> pdb=" O THR A 337 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 350 removed outlier: 4.692A pdb=" N SER A 348 " --> pdb=" O GLU A 345 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LYS A 350 " --> pdb=" O LEU A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 361 through 379 removed outlier: 3.953A pdb=" N ALA A 373 " --> pdb=" O GLN A 369 " (cutoff:3.500A) Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 418 through 429 Processing helix chain 'A' and resid 454 through 461 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 102 through 113 Processing helix chain 'B' and resid 132 through 141 Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 186 through 192 Processing helix chain 'B' and resid 208 through 214 removed outlier: 3.677A pdb=" N ALA B 214 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 251 Processing helix chain 'B' and resid 267 through 270 Processing helix chain 'B' and resid 278 through 284 Processing helix chain 'B' and resid 309 through 316 Processing helix chain 'B' and resid 319 through 324 removed outlier: 4.300A pdb=" N ALA B 323 " --> pdb=" O PRO B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 340 removed outlier: 3.525A pdb=" N LEU B 340 " --> pdb=" O ALA B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 350 removed outlier: 4.539A pdb=" N SER B 348 " --> pdb=" O GLU B 345 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS B 350 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 357 Processing helix chain 'B' and resid 361 through 379 removed outlier: 4.004A pdb=" N ALA B 373 " --> pdb=" O GLN B 369 " (cutoff:3.500A) Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 418 through 429 Processing helix chain 'B' and resid 454 through 461 Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 132 through 141 Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 186 through 192 Processing helix chain 'C' and resid 208 through 214 removed outlier: 3.682A pdb=" N ALA C 214 " --> pdb=" O ASP C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 251 Processing helix chain 'C' and resid 267 through 270 Processing helix chain 'C' and resid 278 through 284 Processing helix chain 'C' and resid 309 through 316 Processing helix chain 'C' and resid 319 through 324 removed outlier: 4.319A pdb=" N ALA C 323 " --> pdb=" O PRO C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 342 removed outlier: 3.569A pdb=" N LEU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR C 341 " --> pdb=" O THR C 337 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 350 removed outlier: 4.604A pdb=" N SER C 348 " --> pdb=" O GLU C 345 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS C 350 " --> pdb=" O LEU C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 357 Processing helix chain 'C' and resid 361 through 378 removed outlier: 3.724A pdb=" N ALA C 373 " --> pdb=" O GLN C 369 " (cutoff:3.500A) Proline residue: C 374 - end of helix Processing helix chain 'C' and resid 418 through 429 Processing helix chain 'C' and resid 454 through 462 Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 102 through 113 Processing helix chain 'D' and resid 132 through 141 Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 186 through 192 Processing helix chain 'D' and resid 208 through 214 removed outlier: 3.693A pdb=" N ALA D 214 " --> pdb=" O ASP D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 251 Processing helix chain 'D' and resid 267 through 270 Processing helix chain 'D' and resid 278 through 284 Processing helix chain 'D' and resid 309 through 316 Processing helix chain 'D' and resid 319 through 323 removed outlier: 4.267A pdb=" N ALA D 323 " --> pdb=" O PRO D 319 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 319 through 323' Processing helix chain 'D' and resid 328 through 340 Processing helix chain 'D' and resid 344 through 350 removed outlier: 4.185A pdb=" N SER D 348 " --> pdb=" O PRO D 344 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLU D 349 " --> pdb=" O GLU D 345 " (cutoff:3.500A) Processing helix chain 'D' and resid 352 through 357 Processing helix chain 'D' and resid 361 through 379 removed outlier: 4.068A pdb=" N ALA D 373 " --> pdb=" O GLN D 369 " (cutoff:3.500A) Proline residue: D 374 - end of helix Processing helix chain 'D' and resid 418 through 429 Processing helix chain 'D' and resid 454 through 462 removed outlier: 3.562A pdb=" N GLU D 459 " --> pdb=" O GLN D 455 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 95 No H-bonds generated for 'chain 'E' and resid 93 through 95' Processing helix chain 'E' and resid 102 through 113 Processing helix chain 'E' and resid 133 through 141 Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 186 through 192 Processing helix chain 'E' and resid 208 through 214 removed outlier: 3.667A pdb=" N ALA E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 251 Processing helix chain 'E' and resid 267 through 270 Processing helix chain 'E' and resid 278 through 284 Processing helix chain 'E' and resid 309 through 316 Processing helix chain 'E' and resid 319 through 324 removed outlier: 4.391A pdb=" N ALA E 323 " --> pdb=" O PRO E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 328 through 342 removed outlier: 3.742A pdb=" N TYR E 341 " --> pdb=" O THR E 337 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 342 " --> pdb=" O LEU E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 344 through 350 removed outlier: 4.575A pdb=" N SER E 348 " --> pdb=" O GLU E 345 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS E 350 " --> pdb=" O LEU E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 357 Processing helix chain 'E' and resid 361 through 377 removed outlier: 3.690A pdb=" N ALA E 373 " --> pdb=" O GLN E 369 " (cutoff:3.500A) Proline residue: E 374 - end of helix Processing helix chain 'E' and resid 423 through 430 removed outlier: 3.561A pdb=" N GLU E 430 " --> pdb=" O ALA E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 458 Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 102 through 113 Processing helix chain 'F' and resid 132 through 141 Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 186 through 192 Processing helix chain 'F' and resid 208 through 214 removed outlier: 3.674A pdb=" N ALA F 214 " --> pdb=" O ASP F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 251 Processing helix chain 'F' and resid 267 through 270 Processing helix chain 'F' and resid 278 through 284 Processing helix chain 'F' and resid 309 through 316 Processing helix chain 'F' and resid 319 through 324 removed outlier: 4.351A pdb=" N ALA F 323 " --> pdb=" O PRO F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 342 removed outlier: 3.716A pdb=" N TYR F 341 " --> pdb=" O THR F 337 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU F 342 " --> pdb=" O LEU F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 350 removed outlier: 4.641A pdb=" N SER F 348 " --> pdb=" O GLU F 345 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS F 350 " --> pdb=" O LEU F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 352 through 357 Processing helix chain 'F' and resid 361 through 373 removed outlier: 3.983A pdb=" N ALA F 373 " --> pdb=" O GLN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 422 through 429 Processing helix chain 'F' and resid 454 through 461 Processing helix chain 'G' and resid 93 through 95 No H-bonds generated for 'chain 'G' and resid 93 through 95' Processing helix chain 'G' and resid 102 through 113 Processing helix chain 'G' and resid 133 through 141 Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 186 through 192 Processing helix chain 'G' and resid 208 through 214 removed outlier: 3.693A pdb=" N ALA G 214 " --> pdb=" O ASP G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 251 Processing helix chain 'G' and resid 267 through 270 Processing helix chain 'G' and resid 278 through 284 Processing helix chain 'G' and resid 309 through 316 Processing helix chain 'G' and resid 319 through 324 removed outlier: 4.318A pdb=" N ALA G 323 " --> pdb=" O PRO G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 340 Processing helix chain 'G' and resid 344 through 350 removed outlier: 4.623A pdb=" N SER G 348 " --> pdb=" O GLU G 345 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS G 350 " --> pdb=" O LEU G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 352 through 357 Processing helix chain 'G' and resid 361 through 379 removed outlier: 4.317A pdb=" N ALA G 373 " --> pdb=" O GLN G 369 " (cutoff:3.500A) Proline residue: G 374 - end of helix Processing helix chain 'G' and resid 418 through 429 Processing helix chain 'G' and resid 448 through 450 No H-bonds generated for 'chain 'G' and resid 448 through 450' Processing helix chain 'G' and resid 454 through 461 Processing helix chain 'H' and resid 93 through 95 No H-bonds generated for 'chain 'H' and resid 93 through 95' Processing helix chain 'H' and resid 102 through 113 Processing helix chain 'H' and resid 132 through 141 Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 186 through 192 Processing helix chain 'H' and resid 208 through 214 removed outlier: 3.668A pdb=" N ALA H 214 " --> pdb=" O ASP H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 251 Processing helix chain 'H' and resid 267 through 270 Processing helix chain 'H' and resid 278 through 284 Processing helix chain 'H' and resid 309 through 316 Processing helix chain 'H' and resid 319 through 324 removed outlier: 4.339A pdb=" N ALA H 323 " --> pdb=" O PRO H 319 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 342 removed outlier: 3.781A pdb=" N TYR H 341 " --> pdb=" O THR H 337 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU H 342 " --> pdb=" O LEU H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 350 removed outlier: 4.499A pdb=" N SER H 348 " --> pdb=" O GLU H 345 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS H 350 " --> pdb=" O LEU H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 352 through 357 Processing helix chain 'H' and resid 361 through 370 Processing helix chain 'H' and resid 422 through 430 removed outlier: 3.619A pdb=" N GLU H 430 " --> pdb=" O ALA H 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 454 through 460 removed outlier: 3.929A pdb=" N GLU H 459 " --> pdb=" O GLN H 455 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET H 460 " --> pdb=" O ARG H 456 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 95 No H-bonds generated for 'chain 'I' and resid 93 through 95' Processing helix chain 'I' and resid 102 through 113 Processing helix chain 'I' and resid 132 through 141 Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 186 through 192 Processing helix chain 'I' and resid 208 through 214 removed outlier: 3.645A pdb=" N ALA I 214 " --> pdb=" O ASP I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 241 through 251 Processing helix chain 'I' and resid 267 through 270 Processing helix chain 'I' and resid 278 through 284 Processing helix chain 'I' and resid 309 through 316 Processing helix chain 'I' and resid 319 through 324 removed outlier: 4.327A pdb=" N ALA I 323 " --> pdb=" O PRO I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 328 through 340 removed outlier: 3.688A pdb=" N LEU I 340 " --> pdb=" O ALA I 336 " (cutoff:3.500A) Processing helix chain 'I' and resid 344 through 350 removed outlier: 4.527A pdb=" N SER I 348 " --> pdb=" O GLU I 345 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS I 350 " --> pdb=" O LEU I 347 " (cutoff:3.500A) Processing helix chain 'I' and resid 352 through 357 Processing helix chain 'I' and resid 361 through 370 Processing helix chain 'I' and resid 422 through 430 Processing helix chain 'I' and resid 454 through 461 Processing helix chain 'J' and resid 93 through 95 No H-bonds generated for 'chain 'J' and resid 93 through 95' Processing helix chain 'J' and resid 102 through 113 Processing helix chain 'J' and resid 132 through 141 Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 186 through 192 Processing helix chain 'J' and resid 208 through 214 removed outlier: 3.664A pdb=" N ALA J 214 " --> pdb=" O ASP J 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 251 Processing helix chain 'J' and resid 267 through 270 Processing helix chain 'J' and resid 278 through 284 Processing helix chain 'J' and resid 309 through 316 Processing helix chain 'J' and resid 319 through 324 removed outlier: 4.305A pdb=" N ALA J 323 " --> pdb=" O PRO J 319 " (cutoff:3.500A) Processing helix chain 'J' and resid 328 through 340 removed outlier: 3.570A pdb=" N LEU J 340 " --> pdb=" O ALA J 336 " (cutoff:3.500A) Processing helix chain 'J' and resid 344 through 350 removed outlier: 4.572A pdb=" N SER J 348 " --> pdb=" O GLU J 345 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS J 350 " --> pdb=" O LEU J 347 " (cutoff:3.500A) Processing helix chain 'J' and resid 352 through 357 Processing helix chain 'J' and resid 361 through 373 removed outlier: 4.080A pdb=" N ALA J 373 " --> pdb=" O GLN J 369 " (cutoff:3.500A) Processing helix chain 'J' and resid 422 through 429 Processing helix chain 'J' and resid 454 through 459 Processing sheet with id= A, first strand: chain 'A' and resid 83 through 85 No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 146 through 150 removed outlier: 3.765A pdb=" N LEU A 288 " --> pdb=" O VAL A 255 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N SER A 292 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLU A 169 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N LEU A 222 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N VAL A 171 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LYS A 224 " --> pdb=" O VAL A 171 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N SER A 173 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N THR A 196 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N VAL A 172 " --> pdb=" O THR A 196 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N HIS A 198 " --> pdb=" O VAL A 172 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 386 through 392 removed outlier: 3.531A pdb=" N LEU A 409 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 150 removed outlier: 3.769A pdb=" N LEU B 288 " --> pdb=" O VAL B 255 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER B 292 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N GLU B 169 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N LEU B 222 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL B 171 " --> pdb=" O LEU B 222 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS B 224 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 8.257A pdb=" N SER B 173 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N THR B 196 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL B 172 " --> pdb=" O THR B 196 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N HIS B 198 " --> pdb=" O VAL B 172 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 383 through 392 Processing sheet with id= F, first strand: chain 'C' and resid 83 through 85 No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'C' and resid 146 through 150 removed outlier: 3.809A pdb=" N LEU C 288 " --> pdb=" O VAL C 255 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER C 292 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N GLU C 169 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 222 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N VAL C 171 " --> pdb=" O LEU C 222 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LYS C 224 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N SER C 173 " --> pdb=" O LYS C 224 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N THR C 196 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL C 172 " --> pdb=" O THR C 196 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N HIS C 198 " --> pdb=" O VAL C 172 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 386 through 392 removed outlier: 3.969A pdb=" N GLN C 386 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 410 " --> pdb=" O GLN C 386 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU C 444 " --> pdb=" O PHE C 411 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 83 through 85 No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 146 through 150 removed outlier: 3.777A pdb=" N LEU D 288 " --> pdb=" O VAL D 255 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N SER D 292 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLU D 169 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU D 222 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N VAL D 171 " --> pdb=" O LEU D 222 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LYS D 224 " --> pdb=" O VAL D 171 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N SER D 173 " --> pdb=" O LYS D 224 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR D 196 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL D 172 " --> pdb=" O THR D 196 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N HIS D 198 " --> pdb=" O VAL D 172 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 387 through 392 removed outlier: 3.855A pdb=" N MET D 388 " --> pdb=" O ALA D 408 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA D 408 " --> pdb=" O MET D 388 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU D 444 " --> pdb=" O PHE D 411 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 83 through 85 No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'E' and resid 146 through 150 removed outlier: 3.751A pdb=" N LEU E 288 " --> pdb=" O VAL E 255 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N SER E 292 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU E 169 " --> pdb=" O ALA E 220 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LEU E 222 " --> pdb=" O GLU E 169 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL E 171 " --> pdb=" O LEU E 222 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LYS E 224 " --> pdb=" O VAL E 171 " (cutoff:3.500A) removed outlier: 8.235A pdb=" N SER E 173 " --> pdb=" O LYS E 224 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N THR E 196 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N VAL E 172 " --> pdb=" O THR E 196 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS E 198 " --> pdb=" O VAL E 172 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 387 through 391 Processing sheet with id= O, first strand: chain 'E' and resid 438 through 440 Processing sheet with id= P, first strand: chain 'F' and resid 83 through 85 No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 146 through 150 removed outlier: 3.769A pdb=" N LEU F 288 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N SER F 292 " --> pdb=" O LEU F 259 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLU F 169 " --> pdb=" O ALA F 220 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU F 222 " --> pdb=" O GLU F 169 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL F 171 " --> pdb=" O LEU F 222 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N LYS F 224 " --> pdb=" O VAL F 171 " (cutoff:3.500A) removed outlier: 8.225A pdb=" N SER F 173 " --> pdb=" O LYS F 224 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N THR F 196 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N VAL F 172 " --> pdb=" O THR F 196 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS F 198 " --> pdb=" O VAL F 172 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 386 through 393 removed outlier: 3.568A pdb=" N LEU F 409 " --> pdb=" O LEU F 446 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU F 444 " --> pdb=" O PHE F 411 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 83 through 85 No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'G' and resid 146 through 150 removed outlier: 3.772A pdb=" N LEU G 288 " --> pdb=" O VAL G 255 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N SER G 292 " --> pdb=" O LEU G 259 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N GLU G 169 " --> pdb=" O ALA G 220 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU G 222 " --> pdb=" O GLU G 169 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL G 171 " --> pdb=" O LEU G 222 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LYS G 224 " --> pdb=" O VAL G 171 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N SER G 173 " --> pdb=" O LYS G 224 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N THR G 196 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N VAL G 172 " --> pdb=" O THR G 196 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N HIS G 198 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 383 through 391 removed outlier: 3.847A pdb=" N ALA G 384 " --> pdb=" O THR G 412 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR G 412 " --> pdb=" O ALA G 384 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN G 386 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR G 410 " --> pdb=" O GLN G 386 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N MET G 388 " --> pdb=" O ALA G 408 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA G 408 " --> pdb=" O MET G 388 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 444 " --> pdb=" O PHE G 411 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 83 through 85 No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'H' and resid 146 through 150 removed outlier: 3.785A pdb=" N LEU H 288 " --> pdb=" O VAL H 255 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N SER H 292 " --> pdb=" O LEU H 259 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N GLU H 169 " --> pdb=" O ALA H 220 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N LEU H 222 " --> pdb=" O GLU H 169 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N VAL H 171 " --> pdb=" O LEU H 222 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N LYS H 224 " --> pdb=" O VAL H 171 " (cutoff:3.500A) removed outlier: 8.309A pdb=" N SER H 173 " --> pdb=" O LYS H 224 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N THR H 196 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL H 172 " --> pdb=" O THR H 196 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N HIS H 198 " --> pdb=" O VAL H 172 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 386 through 391 removed outlier: 3.515A pdb=" N LEU H 409 " --> pdb=" O LEU H 446 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU H 444 " --> pdb=" O PHE H 411 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'I' and resid 83 through 85 No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'I' and resid 146 through 150 removed outlier: 3.744A pdb=" N LEU I 288 " --> pdb=" O VAL I 255 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER I 292 " --> pdb=" O LEU I 259 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N GLU I 169 " --> pdb=" O ALA I 220 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU I 222 " --> pdb=" O GLU I 169 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL I 171 " --> pdb=" O LEU I 222 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS I 224 " --> pdb=" O VAL I 171 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N SER I 173 " --> pdb=" O LYS I 224 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR I 196 " --> pdb=" O VAL I 170 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL I 172 " --> pdb=" O THR I 196 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N HIS I 198 " --> pdb=" O VAL I 172 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'I' and resid 387 through 392 removed outlier: 3.620A pdb=" N LEU I 444 " --> pdb=" O PHE I 411 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'J' and resid 83 through 85 No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'J' and resid 146 through 150 removed outlier: 3.778A pdb=" N LEU J 288 " --> pdb=" O VAL J 255 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER J 292 " --> pdb=" O LEU J 259 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLU J 169 " --> pdb=" O ALA J 220 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU J 222 " --> pdb=" O GLU J 169 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N VAL J 171 " --> pdb=" O LEU J 222 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N LYS J 224 " --> pdb=" O VAL J 171 " (cutoff:3.500A) removed outlier: 8.247A pdb=" N SER J 173 " --> pdb=" O LYS J 224 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N THR J 196 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL J 172 " --> pdb=" O THR J 196 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS J 198 " --> pdb=" O VAL J 172 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'J' and resid 387 through 392 removed outlier: 3.608A pdb=" N LEU J 409 " --> pdb=" O LEU J 446 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU J 444 " --> pdb=" O PHE J 411 " (cutoff:3.500A) 1029 hydrogen bonds defined for protein. 2856 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: 10.43 Time building geometry restraints manager: 12.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.35 - 0.67: 2 0.67 - 0.99: 0 0.99 - 1.31: 4779 1.31 - 1.64: 23645 1.64 - 1.96: 235 Warning: very small bond lengths. Bond restraints: 28661 Sorted by residual: bond pdb=" CG PRO B 389 " pdb=" CD PRO B 389 " ideal model delta sigma weight residual 1.503 0.347 1.156 3.40e-02 8.65e+02 1.16e+03 bond pdb=" CG PRO C 389 " pdb=" CD PRO C 389 " ideal model delta sigma weight residual 1.503 0.587 0.916 3.40e-02 8.65e+02 7.25e+02 bond pdb=" CG PRO F 82 " pdb=" CD PRO F 82 " ideal model delta sigma weight residual 1.503 1.135 0.368 3.40e-02 8.65e+02 1.17e+02 bond pdb=" OP4 LLP F 295 " pdb=" P LLP F 295 " ideal model delta sigma weight residual 1.726 1.538 0.188 2.00e-02 2.50e+03 8.82e+01 bond pdb=" CB PRO C 389 " pdb=" CG PRO C 389 " ideal model delta sigma weight residual 1.492 1.959 -0.467 5.00e-02 4.00e+02 8.73e+01 ... (remaining 28656 not shown) Histogram of bond angle deviations from ideal: 54.24 - 71.16: 2 71.16 - 88.08: 5 88.08 - 105.00: 569 105.00 - 121.92: 32300 121.92 - 138.84: 6026 Bond angle restraints: 38902 Sorted by residual: angle pdb=" N PRO B 389 " pdb=" CD PRO B 389 " pdb=" CG PRO B 389 " ideal model delta sigma weight residual 103.20 54.24 48.96 1.50e+00 4.44e-01 1.07e+03 angle pdb=" N PRO C 389 " pdb=" CD PRO C 389 " pdb=" CG PRO C 389 " ideal model delta sigma weight residual 103.20 60.72 42.48 1.50e+00 4.44e-01 8.02e+02 angle pdb=" N PRO F 82 " pdb=" CD PRO F 82 " pdb=" CG PRO F 82 " ideal model delta sigma weight residual 103.20 82.33 20.87 1.50e+00 4.44e-01 1.94e+02 angle pdb=" CA PRO C 389 " pdb=" CB PRO C 389 " pdb=" CG PRO C 389 " ideal model delta sigma weight residual 104.50 78.17 26.33 1.90e+00 2.77e-01 1.92e+02 angle pdb=" CA PRO B 389 " pdb=" CB PRO B 389 " pdb=" CG PRO B 389 " ideal model delta sigma weight residual 104.50 80.05 24.45 1.90e+00 2.77e-01 1.66e+02 ... (remaining 38897 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.14: 16751 30.14 - 60.29: 769 60.29 - 90.43: 67 90.43 - 120.58: 0 120.58 - 150.72: 2 Dihedral angle restraints: 17589 sinusoidal: 6937 harmonic: 10652 Sorted by residual: dihedral pdb=" CA ASP B 402 " pdb=" C ASP B 402 " pdb=" N ARG B 403 " pdb=" CA ARG B 403 " ideal model delta harmonic sigma weight residual -180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CD LLP B 295 " pdb=" CE LLP B 295 " pdb=" NZ LLP B 295 " pdb=" C4' LLP B 295 " ideal model delta sinusoidal sigma weight residual 249.72 99.00 150.72 1 3.00e+01 1.11e-03 2.00e+01 dihedral pdb=" CD LLP F 295 " pdb=" CE LLP F 295 " pdb=" NZ LLP F 295 " pdb=" C4' LLP F 295 " ideal model delta sinusoidal sigma weight residual 249.72 99.07 150.65 1 3.00e+01 1.11e-03 2.00e+01 ... (remaining 17586 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 3039 0.033 - 0.066: 1127 0.066 - 0.099: 299 0.099 - 0.132: 175 0.132 - 0.165: 11 Chirality restraints: 4651 Sorted by residual: chirality pdb=" CA LEU J 297 " pdb=" N LEU J 297 " pdb=" C LEU J 297 " pdb=" CB LEU J 297 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" CA LEU D 297 " pdb=" N LEU D 297 " pdb=" C LEU D 297 " pdb=" CB LEU D 297 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" CA ASP D 294 " pdb=" N ASP D 294 " pdb=" C ASP D 294 " pdb=" CB ASP D 294 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 4648 not shown) Planarity restraints: 5031 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP E 295 " -0.266 2.00e-02 2.50e+03 3.42e-01 1.17e+03 pdb=" NZ LLP E 295 " 0.555 2.00e-02 2.50e+03 pdb=" C4 LLP E 295 " 0.009 2.00e-02 2.50e+03 pdb=" C4' LLP E 295 " -0.298 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 295 " 0.171 2.00e-02 2.50e+03 3.28e-01 1.08e+03 pdb=" NZ LLP B 295 " -0.464 2.00e-02 2.50e+03 pdb=" C4 LLP B 295 " -0.121 2.00e-02 2.50e+03 pdb=" C4' LLP B 295 " 0.414 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP F 295 " -0.160 2.00e-02 2.50e+03 3.24e-01 1.05e+03 pdb=" NZ LLP F 295 " 0.447 2.00e-02 2.50e+03 pdb=" C4 LLP F 295 " 0.132 2.00e-02 2.50e+03 pdb=" C4' LLP F 295 " -0.420 2.00e-02 2.50e+03 ... (remaining 5028 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 649 2.69 - 3.24: 26654 3.24 - 3.80: 46152 3.80 - 4.35: 62867 4.35 - 4.90: 104467 Nonbonded interactions: 240789 Sorted by model distance: nonbonded pdb=" OP3 LLP E 295 " pdb=" NH1 ARG F 322 " model vdw 2.141 2.496 nonbonded pdb=" OG SER G 392 " pdb=" OD2 ASP G 447 " model vdw 2.167 2.440 nonbonded pdb=" OG SER B 392 " pdb=" OD2 ASP B 447 " model vdw 2.169 2.440 nonbonded pdb=" NH1 ARG A 322 " pdb=" OP3 LLP B 295 " model vdw 2.175 2.496 nonbonded pdb=" OG SER D 392 " pdb=" OD2 ASP D 447 " model vdw 2.178 2.440 ... (remaining 240784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 77 through 120 or resid 129 through 348 or (resid 349 and \ (name N or name CA or name C or name O or name CB )) or resid 350 through 361 or \ (resid 362 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 3 through 371 or resid 387 through 410 or resid 422 through 426 or (resid 427 an \ d (name N or name CA or name C or name O or name CB )) or resid 428 through 429 \ or (resid 430 and (name N or name CA or name C or name O or name CB )) or resid \ 431 through 460)) selection = (chain 'B' and (resid 77 through 120 or resid 129 through 344 or (resid 345 thro \ ugh 346 and (name N or name CA or name C or name O or name CB )) or resid 347 th \ rough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 through 361 or (resid 362 and (name N or name CA or name C or name \ O or name CB )) or resid 363 through 371 or resid 387 through 410 or resid 422 \ through 426 or (resid 427 and (name N or name CA or name C or name O or name CB \ )) or resid 428 through 429 or (resid 430 and (name N or name CA or name C or na \ me O or name CB )) or resid 431 through 454 or (resid 455 and (name N or name CA \ or name C or name O or name CB )) or resid 456 through 460)) selection = (chain 'C' and (resid 77 through 120 or resid 129 through 371 or resid 387 throu \ gh 410 or resid 422 through 426 or (resid 427 and (name N or name CA or name C o \ r name O or name CB )) or resid 428 through 454 or (resid 455 and (name N or nam \ e CA or name C or name O or name CB )) or resid 456 through 460)) selection = (chain 'D' and (resid 77 through 120 or resid 129 through 344 or (resid 345 thro \ ugh 346 and (name N or name CA or name C or name O or name CB )) or resid 347 th \ rough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 through 361 or (resid 362 and (name N or name CA or name C or name \ O or name CB )) or resid 363 through 371 or resid 387 through 410 or resid 422 \ through 426 or (resid 427 and (name N or name CA or name C or name O or name CB \ )) or resid 428 through 429 or (resid 430 and (name N or name CA or name C or na \ me O or name CB )) or resid 431 through 454 or (resid 455 and (name N or name CA \ or name C or name O or name CB )) or resid 456 through 460)) selection = (chain 'E' and (resid 77 through 344 or (resid 345 through 346 and (name N or na \ me CA or name C or name O or name CB )) or resid 347 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O or name CB )) or resid 350 through 361 \ or (resid 362 and (name N or name CA or name C or name O or name CB )) or resid \ 363 through 371 or resid 387 through 426 or (resid 427 and (name N or name CA o \ r name C or name O or name CB )) or resid 428 through 429 or (resid 430 and (nam \ e N or name CA or name C or name O or name CB )) or resid 431 through 454 or (re \ sid 455 and (name N or name CA or name C or name O or name CB )) or resid 456 th \ rough 460)) selection = (chain 'F' and (resid 77 through 120 or resid 129 through 348 or (resid 349 and \ (name N or name CA or name C or name O or name CB )) or resid 350 through 361 or \ (resid 362 and (name N or name CA or name C or name O or name CB )) or resid 36 \ 3 through 371 or resid 387 through 410 or resid 422 through 426 or (resid 427 an \ d (name N or name CA or name C or name O or name CB )) or resid 428 through 429 \ or (resid 430 and (name N or name CA or name C or name O or name CB )) or resid \ 431 through 454 or (resid 455 and (name N or name CA or name C or name O or name \ CB )) or resid 456 through 460)) selection = (chain 'G' and (resid 77 through 344 or (resid 345 through 346 and (name N or na \ me CA or name C or name O or name CB )) or resid 347 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O or name CB )) or resid 350 through 361 \ or (resid 362 and (name N or name CA or name C or name O or name CB )) or resid \ 363 through 371 or resid 387 through 410 or resid 422 through 426 or (resid 427 \ and (name N or name CA or name C or name O or name CB )) or resid 428 through 4 \ 29 or (resid 430 and (name N or name CA or name C or name O or name CB )) or res \ id 431 through 454 or (resid 455 and (name N or name CA or name C or name O or n \ ame CB )) or resid 456 through 460)) selection = (chain 'H' and (resid 77 through 120 or resid 129 through 344 or (resid 345 thro \ ugh 346 and (name N or name CA or name C or name O or name CB )) or resid 347 th \ rough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 through 361 or (resid 362 and (name N or name CA or name C or name \ O or name CB )) or resid 363 through 371 or resid 387 through 410 or resid 422 \ through 429 or (resid 430 and (name N or name CA or name C or name O or name CB \ )) or resid 431 through 454 or (resid 455 and (name N or name CA or name C or na \ me O or name CB )) or resid 456 through 460)) selection = (chain 'I' and (resid 77 through 120 or resid 129 through 344 or (resid 345 thro \ ugh 346 and (name N or name CA or name C or name O or name CB )) or resid 347 th \ rough 348 or (resid 349 and (name N or name CA or name C or name O or name CB )) \ or resid 350 through 361 or (resid 362 and (name N or name CA or name C or name \ O or name CB )) or resid 363 through 371 or resid 387 through 410 or resid 422 \ through 429 or (resid 430 and (name N or name CA or name C or name O or name CB \ )) or resid 431 through 454 or (resid 455 and (name N or name CA or name C or na \ me O or name CB )) or resid 456 through 460)) selection = (chain 'J' and (resid 77 through 344 or (resid 345 through 346 and (name N or na \ me CA or name C or name O or name CB )) or resid 347 through 348 or (resid 349 a \ nd (name N or name CA or name C or name O or name CB )) or resid 350 through 361 \ or (resid 362 and (name N or name CA or name C or name O or name CB )) or resid \ 363 through 371 or resid 387 through 410 or resid 422 through 429 or (resid 430 \ and (name N or name CA or name C or name O or name CB )) or resid 431 through 4 \ 54 or (resid 455 and (name N or name CA or name C or name O or name CB )) or res \ id 456 through 460)) } 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: 9.830 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: 24.300 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 75.950 Find NCS groups from input model: 2.350 Set up NCS constraints: 0.110 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:11.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 124.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 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 : 0.012 1.156 28661 Z= 0.678 Angle : 0.859 48.956 38902 Z= 0.459 Chirality : 0.041 0.165 4651 Planarity : 0.011 0.342 5031 Dihedral : 15.672 150.720 10687 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.71 % Allowed : 12.20 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.14), residues: 3625 helix: 1.18 (0.14), residues: 1443 sheet: 0.31 (0.23), residues: 472 loop : 0.14 (0.16), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP J 445 HIS 0.003 0.001 HIS H 129 PHE 0.015 0.001 PHE G 291 TYR 0.012 0.002 TYR A 230 ARG 0.008 0.001 ARG F 81 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 284 time to evaluate : 3.279 Fit side-chains REVERT: B 275 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6761 (mm-30) REVERT: C 132 ARG cc_start: 0.7642 (mmp80) cc_final: 0.7432 (mmp80) REVERT: E 275 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6621 (mm-30) REVERT: E 389 PRO cc_start: 0.6695 (Cg_exo) cc_final: 0.6443 (Cg_endo) REVERT: F 132 ARG cc_start: 0.7675 (tpp-160) cc_final: 0.7462 (mmp80) REVERT: G 389 PRO cc_start: 0.6833 (Cg_exo) cc_final: 0.6520 (Cg_endo) REVERT: H 389 PRO cc_start: 0.7069 (Cg_exo) cc_final: 0.6834 (Cg_endo) REVERT: H 460 MET cc_start: 0.6143 (mmt) cc_final: 0.5716 (mpt) REVERT: J 403 ARG cc_start: 0.7450 (ttm170) cc_final: 0.7229 (ttm170) outliers start: 21 outliers final: 13 residues processed: 301 average time/residue: 1.4724 time to fit residues: 516.4982 Evaluate side-chains 293 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 280 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 388 MET Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 317 SER Chi-restraints excluded: chain D residue 110 GLN Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain G residue 398 SER Chi-restraints excluded: chain H residue 84 ILE Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain J residue 110 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 310 optimal weight: 6.9990 chunk 278 optimal weight: 0.9980 chunk 154 optimal weight: 0.9990 chunk 95 optimal weight: 0.3980 chunk 188 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 288 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 175 optimal weight: 0.9980 chunk 214 optimal weight: 0.8980 chunk 334 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** B 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 218 ASN E 367 GLN F 207 HIS F 367 GLN G 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.0370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28661 Z= 0.201 Angle : 0.512 9.228 38902 Z= 0.242 Chirality : 0.040 0.135 4651 Planarity : 0.004 0.077 5031 Dihedral : 6.908 97.086 4105 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.08 % Allowed : 12.43 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.82 (0.14), residues: 3625 helix: 1.22 (0.14), residues: 1451 sheet: 0.41 (0.23), residues: 471 loop : 0.11 (0.16), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 445 HIS 0.004 0.000 HIS G 129 PHE 0.014 0.001 PHE D 291 TYR 0.010 0.001 TYR A 230 ARG 0.004 0.000 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 287 time to evaluate : 3.276 Fit side-chains REVERT: B 275 GLU cc_start: 0.7385 (mm-30) cc_final: 0.6794 (mm-30) REVERT: B 460 MET cc_start: 0.6403 (tpp) cc_final: 0.6191 (tpt) REVERT: C 217 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.6975 (mm-30) REVERT: E 275 GLU cc_start: 0.7284 (mm-30) cc_final: 0.6680 (mm-30) REVERT: G 110 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7143 (tt0) REVERT: H 335 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: H 460 MET cc_start: 0.6085 (mmt) cc_final: 0.5666 (mpt) outliers start: 62 outliers final: 20 residues processed: 322 average time/residue: 1.4448 time to fit residues: 544.2681 Evaluate side-chains 298 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 275 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 110 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 185 optimal weight: 0.4980 chunk 103 optimal weight: 4.9990 chunk 278 optimal weight: 0.9990 chunk 227 optimal weight: 0.3980 chunk 92 optimal weight: 4.9990 chunk 334 optimal weight: 0.7980 chunk 361 optimal weight: 10.0000 chunk 298 optimal weight: 7.9990 chunk 331 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 218 ASN B 129 HIS D 207 HIS E 207 HIS E 218 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN H 207 HIS ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.0543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 28661 Z= 0.207 Angle : 0.508 10.208 38902 Z= 0.239 Chirality : 0.040 0.136 4651 Planarity : 0.003 0.050 5031 Dihedral : 6.338 95.329 4081 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.49 % Allowed : 13.34 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.83 (0.14), residues: 3625 helix: 1.24 (0.14), residues: 1448 sheet: 0.39 (0.23), residues: 471 loop : 0.10 (0.16), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 445 HIS 0.004 0.000 HIS G 129 PHE 0.014 0.001 PHE D 291 TYR 0.011 0.001 TYR A 230 ARG 0.004 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 278 time to evaluate : 3.322 Fit side-chains REVERT: A 460 MET cc_start: 0.6455 (tpp) cc_final: 0.6019 (tpt) REVERT: B 275 GLU cc_start: 0.7407 (mm-30) cc_final: 0.6839 (mm-30) REVERT: B 460 MET cc_start: 0.6405 (tpp) cc_final: 0.6183 (tpt) REVERT: C 217 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7021 (mm-30) REVERT: E 275 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6668 (mm-30) REVERT: E 460 MET cc_start: 0.4321 (OUTLIER) cc_final: 0.3769 (mmp) REVERT: G 110 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7138 (tt0) REVERT: G 131 ASP cc_start: 0.7303 (OUTLIER) cc_final: 0.7034 (p0) REVERT: H 94 ASN cc_start: 0.7061 (m-40) cc_final: 0.6824 (m-40) REVERT: H 335 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7462 (tt0) REVERT: I 388 MET cc_start: 0.5862 (OUTLIER) cc_final: 0.5594 (mtm) outliers start: 74 outliers final: 35 residues processed: 322 average time/residue: 1.4463 time to fit residues: 547.7960 Evaluate side-chains 314 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 273 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 305 ILE Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 330 optimal weight: 6.9990 chunk 251 optimal weight: 3.9990 chunk 173 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 224 optimal weight: 5.9990 chunk 335 optimal weight: 0.7980 chunk 355 optimal weight: 2.9990 chunk 175 optimal weight: 0.5980 chunk 318 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 218 ASN D 218 ASN E 218 ASN G 218 ASN ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28661 Z= 0.292 Angle : 0.560 11.892 38902 Z= 0.265 Chirality : 0.042 0.157 4651 Planarity : 0.004 0.050 5031 Dihedral : 6.527 103.947 4081 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.09 % Allowed : 13.91 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.14), residues: 3625 helix: 1.08 (0.14), residues: 1441 sheet: 0.33 (0.23), residues: 463 loop : 0.02 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 445 HIS 0.005 0.001 HIS G 129 PHE 0.019 0.002 PHE A 291 TYR 0.014 0.002 TYR A 230 ARG 0.010 0.001 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 288 time to evaluate : 3.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 460 MET cc_start: 0.6514 (tpp) cc_final: 0.6037 (tpt) REVERT: B 275 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.6909 (mm-30) REVERT: C 217 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7013 (mm-30) REVERT: C 343 HIS cc_start: 0.6806 (m-70) cc_final: 0.6167 (t-170) REVERT: D 327 ASP cc_start: 0.6833 (t0) cc_final: 0.6544 (m-30) REVERT: E 275 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6681 (mm-30) REVERT: F 106 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6724 (tp30) REVERT: G 110 GLN cc_start: 0.7463 (OUTLIER) cc_final: 0.7162 (tt0) REVERT: H 94 ASN cc_start: 0.7107 (m-40) cc_final: 0.6889 (m-40) REVERT: H 217 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6938 (mm-30) REVERT: H 233 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7462 (mm-40) REVERT: H 275 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6954 (mm-30) REVERT: H 335 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7584 (tt0) REVERT: I 388 MET cc_start: 0.5910 (OUTLIER) cc_final: 0.5626 (mtm) REVERT: J 343 HIS cc_start: 0.6813 (m-70) cc_final: 0.6172 (t-170) outliers start: 92 outliers final: 35 residues processed: 339 average time/residue: 1.4681 time to fit residues: 581.1726 Evaluate side-chains 325 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 280 time to evaluate : 3.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 233 GLN Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 296 optimal weight: 4.9990 chunk 201 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 303 optimal weight: 0.5980 chunk 245 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 181 optimal weight: 1.9990 chunk 319 optimal weight: 0.6980 chunk 89 optimal weight: 0.0030 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 218 ASN D 218 ASN E 218 ASN F 218 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 129 HIS G 218 ASN ** I 129 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 28661 Z= 0.256 Angle : 0.535 10.862 38902 Z= 0.252 Chirality : 0.041 0.192 4651 Planarity : 0.003 0.048 5031 Dihedral : 6.436 102.805 4081 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.76 % Allowed : 14.82 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.61 (0.14), residues: 3625 helix: 1.08 (0.14), residues: 1441 sheet: 0.31 (0.22), residues: 471 loop : -0.03 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 445 HIS 0.004 0.001 HIS G 129 PHE 0.017 0.001 PHE D 291 TYR 0.012 0.002 TYR E 230 ARG 0.006 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 284 time to evaluate : 3.289 Fit side-chains REVERT: B 275 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6930 (mm-30) REVERT: C 217 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7066 (mm-30) REVERT: C 343 HIS cc_start: 0.6809 (m-70) cc_final: 0.6150 (t-170) REVERT: D 131 ASP cc_start: 0.7741 (p0) cc_final: 0.7363 (p0) REVERT: D 327 ASP cc_start: 0.6784 (t0) cc_final: 0.6508 (m-30) REVERT: E 275 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6682 (mm-30) REVERT: E 460 MET cc_start: 0.4112 (OUTLIER) cc_final: 0.3652 (mmp) REVERT: F 106 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6612 (tp30) REVERT: G 110 GLN cc_start: 0.7448 (OUTLIER) cc_final: 0.7148 (tt0) REVERT: G 131 ASP cc_start: 0.7398 (OUTLIER) cc_final: 0.7146 (p0) REVERT: H 94 ASN cc_start: 0.7084 (m-40) cc_final: 0.6869 (m-40) REVERT: H 217 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.6936 (mm-30) REVERT: H 233 GLN cc_start: 0.7764 (OUTLIER) cc_final: 0.7478 (mm-40) REVERT: H 275 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6963 (mm-30) REVERT: H 335 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7527 (tt0) REVERT: I 335 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: J 110 GLN cc_start: 0.7165 (OUTLIER) cc_final: 0.6800 (tt0) REVERT: J 131 ASP cc_start: 0.7546 (p0) cc_final: 0.7210 (p0) REVERT: J 343 HIS cc_start: 0.6968 (m-70) cc_final: 0.6380 (t-170) outliers start: 82 outliers final: 42 residues processed: 335 average time/residue: 1.4305 time to fit residues: 560.6835 Evaluate side-chains 334 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 280 time to evaluate : 3.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 240 ASP Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 110 GLN Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 233 GLN Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 354 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 305 ILE Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 119 optimal weight: 2.9990 chunk 320 optimal weight: 0.6980 chunk 70 optimal weight: 7.9990 chunk 208 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 356 optimal weight: 0.6980 chunk 295 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 29 optimal weight: 0.0870 chunk 117 optimal weight: 2.9990 chunk 186 optimal weight: 0.3980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 218 ASN D 218 ASN E 218 ASN F 218 ASN G 218 ASN I 129 HIS J 218 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.077 28661 Z= 0.156 Angle : 0.479 8.338 38902 Z= 0.226 Chirality : 0.039 0.210 4651 Planarity : 0.003 0.047 5031 Dihedral : 6.166 94.535 4081 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.65 % Allowed : 15.32 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.80 (0.14), residues: 3625 helix: 1.27 (0.14), residues: 1444 sheet: 0.38 (0.22), residues: 482 loop : 0.05 (0.16), residues: 1699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 445 HIS 0.002 0.000 HIS I 129 PHE 0.010 0.001 PHE B 291 TYR 0.009 0.001 TYR F 230 ARG 0.007 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 285 time to evaluate : 3.291 Fit side-chains revert: symmetry clash REVERT: B 275 GLU cc_start: 0.7523 (mm-30) cc_final: 0.6951 (mm-30) REVERT: B 460 MET cc_start: 0.6600 (tpp) cc_final: 0.6361 (tpt) REVERT: C 217 GLU cc_start: 0.7591 (OUTLIER) cc_final: 0.7110 (mm-30) REVERT: D 131 ASP cc_start: 0.7721 (p0) cc_final: 0.7373 (p0) REVERT: D 388 MET cc_start: 0.6744 (OUTLIER) cc_final: 0.5030 (tmt) REVERT: E 275 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6685 (mm-30) REVERT: E 460 MET cc_start: 0.4115 (OUTLIER) cc_final: 0.3608 (mmp) REVERT: G 110 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: G 131 ASP cc_start: 0.7327 (OUTLIER) cc_final: 0.7007 (p0) REVERT: G 461 LEU cc_start: 0.7803 (OUTLIER) cc_final: 0.7441 (tp) REVERT: H 217 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6865 (mm-30) REVERT: H 335 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: I 132 ARG cc_start: 0.7196 (tpp-160) cc_final: 0.6935 (tpp-160) REVERT: J 131 ASP cc_start: 0.7504 (p0) cc_final: 0.7060 (p0) REVERT: J 343 HIS cc_start: 0.6814 (m-70) cc_final: 0.6161 (t-170) outliers start: 79 outliers final: 35 residues processed: 335 average time/residue: 1.3666 time to fit residues: 539.5984 Evaluate side-chains 315 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 272 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 383 PHE Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 409 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 343 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 202 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 201 optimal weight: 0.3980 chunk 299 optimal weight: 8.9990 chunk 198 optimal weight: 1.9990 chunk 354 optimal weight: 0.6980 chunk 221 optimal weight: 8.9990 chunk 216 optimal weight: 10.0000 chunk 163 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN A 218 ASN D 218 ASN E 218 ASN F 218 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28661 Z= 0.209 Angle : 0.515 9.439 38902 Z= 0.241 Chirality : 0.040 0.224 4651 Planarity : 0.003 0.045 5031 Dihedral : 6.198 98.927 4078 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.62 % Allowed : 15.89 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.78 (0.14), residues: 3625 helix: 1.25 (0.14), residues: 1439 sheet: 0.37 (0.22), residues: 484 loop : 0.04 (0.16), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP J 445 HIS 0.004 0.000 HIS I 129 PHE 0.014 0.001 PHE D 291 TYR 0.011 0.001 TYR A 230 ARG 0.014 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 281 time to evaluate : 2.862 Fit side-chains revert: symmetry clash REVERT: A 309 LYS cc_start: 0.7681 (tttp) cc_final: 0.7470 (tttp) REVERT: B 275 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6976 (mm-30) REVERT: B 460 MET cc_start: 0.6656 (tpp) cc_final: 0.6453 (tpt) REVERT: C 217 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: C 343 HIS cc_start: 0.6777 (m-70) cc_final: 0.6183 (t-170) REVERT: D 190 MET cc_start: 0.8500 (ttm) cc_final: 0.8237 (mtp) REVERT: D 388 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.4977 (tmt) REVERT: E 275 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6633 (mm-30) REVERT: E 460 MET cc_start: 0.4078 (OUTLIER) cc_final: 0.3596 (mmp) REVERT: F 106 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6532 (tp30) REVERT: G 110 GLN cc_start: 0.7422 (OUTLIER) cc_final: 0.7121 (tt0) REVERT: G 131 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.7179 (p0) REVERT: H 81 ARG cc_start: 0.6884 (ptm160) cc_final: 0.6535 (ptm-80) REVERT: H 217 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.6962 (mm-30) REVERT: H 275 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6970 (mm-30) REVERT: H 335 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: H 354 LEU cc_start: 0.6819 (mt) cc_final: 0.6605 (mp) REVERT: J 131 ASP cc_start: 0.7560 (p0) cc_final: 0.7068 (p0) REVERT: J 343 HIS cc_start: 0.6887 (m-70) cc_final: 0.6245 (t-170) outliers start: 78 outliers final: 46 residues processed: 334 average time/residue: 1.4517 time to fit residues: 568.4564 Evaluate side-chains 331 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 276 time to evaluate : 3.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 409 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 240 ASP Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 383 PHE Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain H residue 404 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 110 GLN Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 305 ILE Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 451 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 219 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 69 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 225 optimal weight: 5.9990 chunk 241 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 33 optimal weight: 9.9990 chunk 278 optimal weight: 0.0000 overall best weight: 1.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN C 92 HIS D 218 ASN E 218 ASN F 94 ASN F 218 ASN G 218 ASN J 218 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 28661 Z= 0.284 Angle : 0.560 11.069 38902 Z= 0.263 Chirality : 0.042 0.233 4651 Planarity : 0.004 0.050 5031 Dihedral : 6.365 105.692 4078 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.62 % Allowed : 15.99 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.14), residues: 3625 helix: 1.09 (0.14), residues: 1444 sheet: 0.34 (0.22), residues: 483 loop : -0.05 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 445 HIS 0.004 0.001 HIS I 129 PHE 0.018 0.001 PHE D 291 TYR 0.013 0.002 TYR A 230 ARG 0.013 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 274 time to evaluate : 3.160 Fit side-chains REVERT: A 309 LYS cc_start: 0.7647 (tttp) cc_final: 0.7423 (tttp) REVERT: B 275 GLU cc_start: 0.7505 (mm-30) cc_final: 0.6981 (mm-30) REVERT: B 460 MET cc_start: 0.6637 (tpp) cc_final: 0.6377 (tpt) REVERT: C 217 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7093 (mm-30) REVERT: D 112 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.8233 (mtm) REVERT: D 131 ASP cc_start: 0.7729 (p0) cc_final: 0.7504 (p0) REVERT: D 190 MET cc_start: 0.8514 (ttm) cc_final: 0.8266 (mtp) REVERT: D 327 ASP cc_start: 0.6840 (t0) cc_final: 0.6581 (m-30) REVERT: E 275 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6613 (mm-30) REVERT: E 460 MET cc_start: 0.4131 (OUTLIER) cc_final: 0.3643 (mmp) REVERT: F 106 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6632 (tp30) REVERT: G 110 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7154 (tt0) REVERT: G 131 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7216 (p0) REVERT: G 461 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7447 (tp) REVERT: H 217 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7004 (mm-30) REVERT: H 233 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7401 (mm-40) REVERT: H 275 GLU cc_start: 0.7389 (OUTLIER) cc_final: 0.7001 (mm-30) REVERT: H 335 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: I 132 ARG cc_start: 0.7313 (tpp-160) cc_final: 0.7078 (tpp-160) REVERT: I 335 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7564 (tt0) REVERT: J 343 HIS cc_start: 0.7021 (m-70) cc_final: 0.6403 (t-170) REVERT: J 388 MET cc_start: 0.5760 (OUTLIER) cc_final: 0.5504 (ptt) outliers start: 78 outliers final: 42 residues processed: 323 average time/residue: 1.4117 time to fit residues: 535.0943 Evaluate side-chains 330 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 274 time to evaluate : 3.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 310 GLU Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 383 PHE Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 233 GLN Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 335 GLU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 354 LEU Chi-restraints excluded: chain J residue 388 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 322 optimal weight: 0.6980 chunk 339 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 330 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 143 optimal weight: 9.9990 chunk 259 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 298 optimal weight: 0.9980 chunk 312 optimal weight: 0.7980 chunk 329 optimal weight: 4.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN D 218 ASN E 218 ASN F 218 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN H 92 HIS J 92 HIS J 218 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28661 Z= 0.227 Angle : 0.530 9.847 38902 Z= 0.247 Chirality : 0.040 0.209 4651 Planarity : 0.003 0.050 5031 Dihedral : 6.228 103.047 4078 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.25 % Allowed : 16.94 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.64 (0.14), residues: 3625 helix: 1.11 (0.14), residues: 1451 sheet: 0.36 (0.22), residues: 482 loop : -0.05 (0.15), residues: 1692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP J 445 HIS 0.004 0.000 HIS I 129 PHE 0.016 0.001 PHE G 291 TYR 0.012 0.001 TYR I 230 ARG 0.013 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 273 time to evaluate : 3.039 Fit side-chains REVERT: A 309 LYS cc_start: 0.7614 (tttp) cc_final: 0.7370 (tttp) REVERT: B 460 MET cc_start: 0.6648 (tpp) cc_final: 0.6385 (tpt) REVERT: C 217 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7096 (mm-30) REVERT: D 106 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6638 (tp30) REVERT: D 112 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.8224 (mtm) REVERT: D 131 ASP cc_start: 0.7697 (p0) cc_final: 0.7067 (p0) REVERT: D 190 MET cc_start: 0.8476 (ttm) cc_final: 0.8216 (mtp) REVERT: D 327 ASP cc_start: 0.6816 (t0) cc_final: 0.6542 (m-30) REVERT: E 275 GLU cc_start: 0.7235 (OUTLIER) cc_final: 0.6642 (mm-30) REVERT: E 460 MET cc_start: 0.4129 (OUTLIER) cc_final: 0.3642 (mmp) REVERT: F 106 GLU cc_start: 0.6924 (OUTLIER) cc_final: 0.6542 (tp30) REVERT: G 110 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7124 (tt0) REVERT: G 131 ASP cc_start: 0.7391 (OUTLIER) cc_final: 0.7102 (p0) REVERT: G 461 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7432 (tp) REVERT: H 81 ARG cc_start: 0.6877 (ptm160) cc_final: 0.6665 (ptm-80) REVERT: H 217 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6959 (mm-30) REVERT: H 233 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7382 (mm-40) REVERT: H 275 GLU cc_start: 0.7400 (OUTLIER) cc_final: 0.7009 (mm-30) REVERT: H 335 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7530 (tt0) REVERT: J 131 ASP cc_start: 0.7540 (p0) cc_final: 0.7147 (p0) REVERT: J 343 HIS cc_start: 0.6992 (m-70) cc_final: 0.6377 (t-170) outliers start: 67 outliers final: 47 residues processed: 317 average time/residue: 1.4870 time to fit residues: 553.2202 Evaluate side-chains 327 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 267 time to evaluate : 3.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 106 GLU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 354 LEU Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 275 GLU Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain G residue 354 LEU Chi-restraints excluded: chain G residue 383 PHE Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 233 GLN Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 217 optimal weight: 0.6980 chunk 349 optimal weight: 0.8980 chunk 213 optimal weight: 1.9990 chunk 165 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 366 optimal weight: 7.9990 chunk 337 optimal weight: 0.5980 chunk 291 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 225 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN D 218 ASN D 367 GLN E 218 ASN F 218 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN J 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 28661 Z= 0.195 Angle : 0.513 8.915 38902 Z= 0.240 Chirality : 0.040 0.205 4651 Planarity : 0.003 0.049 5031 Dihedral : 6.129 100.218 4078 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.02 % Allowed : 17.17 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.14), residues: 3625 helix: 1.19 (0.14), residues: 1449 sheet: 0.35 (0.22), residues: 491 loop : -0.03 (0.16), residues: 1685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 445 HIS 0.004 0.000 HIS I 129 PHE 0.014 0.001 PHE G 291 TYR 0.010 0.001 TYR I 230 ARG 0.013 0.000 ARG B 403 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7250 Ramachandran restraints generated. 3625 Oldfield, 0 Emsley, 3625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 270 time to evaluate : 3.290 Fit side-chains REVERT: A 309 LYS cc_start: 0.7601 (tttp) cc_final: 0.7360 (tttp) REVERT: B 275 GLU cc_start: 0.7552 (mm-30) cc_final: 0.6978 (mm-30) REVERT: B 460 MET cc_start: 0.6651 (tpp) cc_final: 0.6390 (tpt) REVERT: C 132 ARG cc_start: 0.7632 (mmp80) cc_final: 0.7301 (mmp80) REVERT: C 217 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7161 (mm-30) REVERT: D 112 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8226 (mtm) REVERT: D 131 ASP cc_start: 0.7692 (p0) cc_final: 0.7011 (p0) REVERT: D 190 MET cc_start: 0.8467 (ttm) cc_final: 0.8237 (mtp) REVERT: D 327 ASP cc_start: 0.6726 (t0) cc_final: 0.6445 (m-30) REVERT: D 388 MET cc_start: 0.6730 (OUTLIER) cc_final: 0.4989 (tmt) REVERT: E 275 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6650 (mm-30) REVERT: E 460 MET cc_start: 0.4128 (OUTLIER) cc_final: 0.3655 (mmp) REVERT: F 106 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6530 (tp30) REVERT: G 110 GLN cc_start: 0.7417 (OUTLIER) cc_final: 0.7114 (tt0) REVERT: G 131 ASP cc_start: 0.7359 (OUTLIER) cc_final: 0.7046 (p0) REVERT: G 461 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7430 (tp) REVERT: H 81 ARG cc_start: 0.6853 (ptm160) cc_final: 0.6633 (ptm-80) REVERT: H 217 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6946 (mm-30) REVERT: H 233 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7388 (mm-40) REVERT: H 275 GLU cc_start: 0.7385 (OUTLIER) cc_final: 0.6988 (mm-30) REVERT: H 335 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7540 (tt0) REVERT: J 131 ASP cc_start: 0.7518 (p0) cc_final: 0.6950 (p0) REVERT: J 343 HIS cc_start: 0.6979 (m-70) cc_final: 0.6364 (t-170) outliers start: 60 outliers final: 45 residues processed: 311 average time/residue: 1.4579 time to fit residues: 530.3648 Evaluate side-chains 325 residues out of total 2988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 268 time to evaluate : 3.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 110 GLN Chi-restraints excluded: chain A residue 451 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 136 GLN Chi-restraints excluded: chain C residue 217 GLU Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 409 LEU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 348 SER Chi-restraints excluded: chain D residue 388 MET Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain E residue 110 GLN Chi-restraints excluded: chain E residue 131 ASP Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 354 LEU Chi-restraints excluded: chain E residue 388 MET Chi-restraints excluded: chain E residue 460 MET Chi-restraints excluded: chain F residue 80 LEU Chi-restraints excluded: chain F residue 106 GLU Chi-restraints excluded: chain F residue 110 GLN Chi-restraints excluded: chain F residue 275 GLU Chi-restraints excluded: chain F residue 305 ILE Chi-restraints excluded: chain F residue 335 GLU Chi-restraints excluded: chain F residue 354 LEU Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 110 GLN Chi-restraints excluded: chain G residue 131 ASP Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 305 ILE Chi-restraints excluded: chain G residue 309 LYS Chi-restraints excluded: chain G residue 383 PHE Chi-restraints excluded: chain G residue 461 LEU Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 110 GLN Chi-restraints excluded: chain H residue 217 GLU Chi-restraints excluded: chain H residue 233 GLN Chi-restraints excluded: chain H residue 275 GLU Chi-restraints excluded: chain H residue 305 ILE Chi-restraints excluded: chain H residue 317 SER Chi-restraints excluded: chain H residue 335 GLU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 86 LEU Chi-restraints excluded: chain I residue 297 LEU Chi-restraints excluded: chain I residue 354 LEU Chi-restraints excluded: chain I residue 388 MET Chi-restraints excluded: chain I residue 409 LEU Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 297 LEU Chi-restraints excluded: chain J residue 354 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 368 random chunks: chunk 231 optimal weight: 2.9990 chunk 310 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 269 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 81 optimal weight: 0.0050 chunk 292 optimal weight: 8.9990 chunk 122 optimal weight: 0.0870 chunk 300 optimal weight: 0.2980 chunk 37 optimal weight: 6.9990 chunk 53 optimal weight: 0.0060 overall best weight: 0.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN D 218 ASN E 218 ASN F 218 ASN ** F 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 218 ASN H 226 HIS J 218 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.203196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.139256 restraints weight = 29660.072| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.22 r_work: 0.3517 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 28661 Z= 0.119 Angle : 0.475 8.696 38902 Z= 0.220 Chirality : 0.039 0.180 4651 Planarity : 0.003 0.048 5031 Dihedral : 5.873 90.040 4078 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.81 % Allowed : 17.47 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.14), residues: 3625 helix: 1.41 (0.14), residues: 1448 sheet: 0.39 (0.23), residues: 470 loop : 0.11 (0.16), residues: 1707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 445 HIS 0.004 0.000 HIS I 129 PHE 0.009 0.001 PHE A 411 TYR 0.007 0.001 TYR E 230 ARG 0.013 0.000 ARG I 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10195.94 seconds wall clock time: 184 minutes 19.55 seconds (11059.55 seconds total)