Starting phenix.real_space_refine on Sat Aug 10 11:53:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/08_2024/5u0a_8478.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/08_2024/5u0a_8478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/08_2024/5u0a_8478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/08_2024/5u0a_8478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/08_2024/5u0a_8478.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/08_2024/5u0a_8478.cif" } resolution = 3.3 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 ------------------------------------------------------------------------------- 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= 0.017 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 143 5.49 5 S 46 5.16 5 C 17670 2.51 5 N 5313 2.21 5 O 5751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C ARG 98": "NH1" <-> "NH2" Residue "C ARG 130": "NH1" <-> "NH2" Residue "C ARG 137": "NH1" <-> "NH2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C ARG 336": "NH1" <-> "NH2" Residue "D ARG 172": "NH1" <-> "NH2" Residue "D ARG 289": "NH1" <-> "NH2" Residue "D ARG 292": "NH1" <-> "NH2" Residue "D GLU 351": "OE1" <-> "OE2" Residue "E TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 135": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ARG 172": "NH1" <-> "NH2" Residue "E GLU 258": "OE1" <-> "OE2" Residue "E ARG 292": "NH1" <-> "NH2" Residue "E ARG 324": "NH1" <-> "NH2" Residue "F ARG 45": "NH1" <-> "NH2" Residue "F ARG 135": "NH1" <-> "NH2" Residue "F ARG 155": "NH1" <-> "NH2" Residue "F ARG 172": "NH1" <-> "NH2" Residue "F ARG 292": "NH1" <-> "NH2" Residue "G ARG 45": "NH1" <-> "NH2" Residue "G ARG 135": "NH1" <-> "NH2" Residue "G ARG 155": "NH1" <-> "NH2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "G ARG 292": "NH1" <-> "NH2" Residue "H TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 45": "NH1" <-> "NH2" Residue "H ARG 135": "NH1" <-> "NH2" Residue "H ARG 155": "NH1" <-> "NH2" Residue "H ARG 172": "NH1" <-> "NH2" Residue "H ARG 292": "NH1" <-> "NH2" Residue "I ARG 45": "NH1" <-> "NH2" Residue "I ARG 135": "NH1" <-> "NH2" Residue "I ARG 155": "NH1" <-> "NH2" Residue "I ARG 172": "NH1" <-> "NH2" Residue "I ARG 292": "NH1" <-> "NH2" Residue "J ARG 32": "NH1" <-> "NH2" Residue "L ARG 28": "NH1" <-> "NH2" Residue "L ARG 32": "NH1" <-> "NH2" Residue "L ARG 211": "NH1" <-> "NH2" Residue "N ARG 47": "NH1" <-> "NH2" Residue "N ARG 172": "NH1" <-> "NH2" Residue "N ARG 217": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 28923 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1439 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 182} Chain breaks: 8 Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 3980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 503, 3980 Classifications: {'peptide': 503} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 41, 'TRANS': 461} Chain breaks: 2 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 2017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2017 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 1 Chain: "E" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2840 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain: "F" Number of atoms: 2840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2840 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 15, 'TRANS': 351} Chain: "G" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2829 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain: "H" Number of atoms: 2829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2829 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 15, 'TRANS': 350} Chain: "I" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2543 Classifications: {'peptide': 329} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "J" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1388 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 2 Chain: "K" Number of atoms: 1267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 1267 Classifications: {'RNA': 59} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 12, 'rna3p_pur': 25, 'rna3p_pyr': 13} Link IDs: {'rna2p': 21, 'rna3p': 37} Chain breaks: 1 Chain: "L" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1322 Classifications: {'peptide': 165} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 157} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1013 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain: "N" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1896 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 20, 'TRANS': 220} Chain breaks: 1 Chain: "O" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 720 Classifications: {'DNA': 35} Link IDs: {'rna3p': 34} Chain breaks: 1 Time building chain proxies: 15.35, per 1000 atoms: 0.53 Number of scatterers: 28923 At special positions: 0 Unit cell: (188.19, 131.61, 145.14, 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 46 16.00 P 143 15.00 O 5751 8.00 N 5313 7.00 C 17670 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=0, symmetry=0 Time building additional restraints: 11.65 Conformation dependent library (CDL) restraints added in 4.7 seconds 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6254 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 32 sheets defined 45.9% alpha, 17.7% beta 28 base pairs and 66 stacking pairs defined. Time for finding SS restraints: 9.19 Creating SS restraints... Processing helix chain 'A' and resid 22 through 32 Processing helix chain 'A' and resid 143 through 154 Processing helix chain 'A' and resid 198 through 209 Processing helix chain 'A' and resid 213 through 217 removed outlier: 3.630A pdb=" N GLY A 217 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 61 through 73 removed outlier: 3.832A pdb=" N ARG C 70 " --> pdb=" O ALA C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 82 Processing helix chain 'C' and resid 89 through 105 Processing helix chain 'C' and resid 108 through 119 removed outlier: 3.673A pdb=" N VAL C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TYR C 119 " --> pdb=" O TYR C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 removed outlier: 3.842A pdb=" N PHE C 123 " --> pdb=" O SER C 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 137 through 142 removed outlier: 3.986A pdb=" N GLU C 141 " --> pdb=" O ARG C 137 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N CYS C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 137 through 142' Processing helix chain 'C' and resid 147 through 152 Processing helix chain 'C' and resid 178 through 191 Processing helix chain 'C' and resid 227 through 235 removed outlier: 3.567A pdb=" N SER C 231 " --> pdb=" O THR C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 271 Processing helix chain 'C' and resid 338 through 345 removed outlier: 3.721A pdb=" N HIS C 343 " --> pdb=" O ALA C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 359 Processing helix chain 'C' and resid 367 through 372 removed outlier: 4.078A pdb=" N SER C 371 " --> pdb=" O GLU C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 396 through 407 removed outlier: 4.517A pdb=" N ARG C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 403 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N GLU C 406 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR C 407 " --> pdb=" O ALA C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 409 through 446 Processing helix chain 'C' and resid 464 through 487 removed outlier: 3.773A pdb=" N HIS C 468 " --> pdb=" O PRO C 464 " (cutoff:3.500A) Proline residue: C 479 - end of helix Processing helix chain 'C' and resid 502 through 516 removed outlier: 3.609A pdb=" N VAL C 507 " --> pdb=" O ALA C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 520 Processing helix chain 'C' and resid 522 through 534 Processing helix chain 'C' and resid 535 through 538 removed outlier: 3.721A pdb=" N SER C 538 " --> pdb=" O THR C 535 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 535 through 538' Processing helix chain 'D' and resid 39 through 55 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 239 through 247 Processing helix chain 'D' and resid 248 through 266 Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 310 through 329 Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 355 through 368 removed outlier: 3.647A pdb=" N PHE D 368 " --> pdb=" O VAL D 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 39 through 56 removed outlier: 3.502A pdb=" N TRP E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 removed outlier: 3.788A pdb=" N GLU E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 79 through 93 Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.938A pdb=" N HIS E 134 " --> pdb=" O ILE E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 144 removed outlier: 3.857A pdb=" N LYS E 144 " --> pdb=" O LYS E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE E 156 " --> pdb=" O PRO E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 Processing helix chain 'E' and resid 239 through 247 Processing helix chain 'E' and resid 248 through 266 Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 309 through 329 removed outlier: 4.242A pdb=" N ARG E 313 " --> pdb=" O GLY E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 346 through 350 removed outlier: 3.588A pdb=" N LEU E 349 " --> pdb=" O LEU E 346 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY E 350 " --> pdb=" O ALA E 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 346 through 350' Processing helix chain 'E' and resid 355 through 368 Processing helix chain 'F' and resid 39 through 56 removed outlier: 3.501A pdb=" N TRP F 43 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 76 removed outlier: 3.719A pdb=" N GLU F 68 " --> pdb=" O ARG F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 93 Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.939A pdb=" N HIS F 134 " --> pdb=" O ILE F 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 144 removed outlier: 3.858A pdb=" N LYS F 144 " --> pdb=" O LYS F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE F 156 " --> pdb=" O PRO F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 171 Processing helix chain 'F' and resid 239 through 247 Processing helix chain 'F' and resid 248 through 266 Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 309 through 329 removed outlier: 4.244A pdb=" N ARG F 313 " --> pdb=" O GLY F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 350 removed outlier: 3.588A pdb=" N LEU F 349 " --> pdb=" O LEU F 346 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY F 350 " --> pdb=" O ALA F 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 346 through 350' Processing helix chain 'F' and resid 355 through 368 Processing helix chain 'G' and resid 39 through 56 removed outlier: 3.502A pdb=" N TRP G 43 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing helix chain 'G' and resid 64 through 76 removed outlier: 3.720A pdb=" N GLU G 68 " --> pdb=" O ARG G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 93 Processing helix chain 'G' and resid 121 through 134 removed outlier: 3.938A pdb=" N HIS G 134 " --> pdb=" O ILE G 130 " (cutoff:3.500A) Processing helix chain 'G' and resid 134 through 144 removed outlier: 3.858A pdb=" N LYS G 144 " --> pdb=" O LYS G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE G 156 " --> pdb=" O PRO G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 171 Processing helix chain 'G' and resid 239 through 247 Processing helix chain 'G' and resid 248 through 266 Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 309 through 329 removed outlier: 4.244A pdb=" N ARG G 313 " --> pdb=" O GLY G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 350 removed outlier: 3.587A pdb=" N LEU G 349 " --> pdb=" O LEU G 346 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY G 350 " --> pdb=" O ALA G 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 346 through 350' Processing helix chain 'G' and resid 355 through 367 Processing helix chain 'H' and resid 39 through 56 removed outlier: 3.501A pdb=" N TRP H 43 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.720A pdb=" N GLU H 68 " --> pdb=" O ARG H 64 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 93 Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.939A pdb=" N HIS H 134 " --> pdb=" O ILE H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 144 removed outlier: 3.857A pdb=" N LYS H 144 " --> pdb=" O LYS H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE H 156 " --> pdb=" O PRO H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 171 Processing helix chain 'H' and resid 239 through 247 Processing helix chain 'H' and resid 248 through 266 Processing helix chain 'H' and resid 271 through 276 Processing helix chain 'H' and resid 296 through 301 Processing helix chain 'H' and resid 309 through 329 removed outlier: 4.244A pdb=" N ARG H 313 " --> pdb=" O GLY H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 removed outlier: 3.586A pdb=" N LEU H 349 " --> pdb=" O LEU H 346 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY H 350 " --> pdb=" O ALA H 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 346 through 350' Processing helix chain 'H' and resid 355 through 367 Processing helix chain 'I' and resid 39 through 56 removed outlier: 3.502A pdb=" N TRP I 43 " --> pdb=" O SER I 39 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 76 removed outlier: 3.720A pdb=" N GLU I 68 " --> pdb=" O ARG I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 79 through 93 Processing helix chain 'I' and resid 121 through 134 removed outlier: 3.939A pdb=" N HIS I 134 " --> pdb=" O ILE I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 134 through 144 removed outlier: 3.858A pdb=" N LYS I 144 " --> pdb=" O LYS I 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 152 through 161 removed outlier: 3.653A pdb=" N ILE I 156 " --> pdb=" O PRO I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 171 Processing helix chain 'I' and resid 239 through 247 Processing helix chain 'I' and resid 248 through 266 Processing helix chain 'I' and resid 296 through 301 Processing helix chain 'I' and resid 309 through 329 removed outlier: 4.243A pdb=" N ARG I 313 " --> pdb=" O GLY I 309 " (cutoff:3.500A) Processing helix chain 'I' and resid 346 through 350 removed outlier: 3.588A pdb=" N LEU I 349 " --> pdb=" O LEU I 346 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY I 350 " --> pdb=" O ALA I 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 346 through 350' Processing helix chain 'I' and resid 355 through 367 Processing helix chain 'J' and resid 6 through 24 removed outlier: 4.033A pdb=" N VAL J 22 " --> pdb=" O SER J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 33 removed outlier: 3.691A pdb=" N ARG J 28 " --> pdb=" O GLU J 24 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 41 through 45 Processing helix chain 'J' and resid 47 through 52 Processing helix chain 'J' and resid 53 through 55 No H-bonds generated for 'chain 'J' and resid 53 through 55' Processing helix chain 'J' and resid 75 through 90 Processing helix chain 'J' and resid 92 through 98 removed outlier: 3.753A pdb=" N GLN J 98 " --> pdb=" O SER J 94 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 149 Processing helix chain 'J' and resid 153 through 165 Processing helix chain 'J' and resid 168 through 186 removed outlier: 3.604A pdb=" N HIS J 173 " --> pdb=" O LEU J 169 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG J 174 " --> pdb=" O ASP J 170 " (cutoff:3.500A) Proline residue: J 177 - end of helix removed outlier: 4.013A pdb=" N ASP J 186 " --> pdb=" O TYR J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 202 Processing helix chain 'J' and resid 209 through 228 removed outlier: 3.554A pdb=" N ALA J 228 " --> pdb=" O LEU J 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 24 removed outlier: 3.694A pdb=" N HIS L 9 " --> pdb=" O TYR L 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 33 Processing helix chain 'L' and resid 45 through 51 Processing helix chain 'L' and resid 75 through 90 removed outlier: 4.089A pdb=" N VAL L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 98 removed outlier: 3.650A pdb=" N GLN L 98 " --> pdb=" O SER L 94 " (cutoff:3.500A) Processing helix chain 'L' and resid 138 through 149 Processing helix chain 'L' and resid 153 through 167 removed outlier: 3.588A pdb=" N GLN L 159 " --> pdb=" O ASP L 155 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN L 167 " --> pdb=" O LEU L 163 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 186 removed outlier: 3.869A pdb=" N HIS L 173 " --> pdb=" O LEU L 169 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG L 174 " --> pdb=" O ASP L 170 " (cutoff:3.500A) Proline residue: L 177 - end of helix Processing helix chain 'L' and resid 191 through 205 removed outlier: 3.881A pdb=" N GLY L 203 " --> pdb=" O LEU L 199 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N HIS L 204 " --> pdb=" O ALA L 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 229 removed outlier: 3.944A pdb=" N VAL L 209 " --> pdb=" O THR L 205 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 44 Processing helix chain 'N' and resid 81 through 85 removed outlier: 3.724A pdb=" N THR N 85 " --> pdb=" O LYS N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 130 Processing helix chain 'N' and resid 157 through 164 removed outlier: 3.785A pdb=" N GLU N 161 " --> pdb=" O ASP N 157 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU N 164 " --> pdb=" O ARG N 160 " (cutoff:3.500A) Processing helix chain 'N' and resid 236 through 248 Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 57 removed outlier: 6.302A pdb=" N TYR A 63 " --> pdb=" O GLU A 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 102 through 103 Processing sheet with id=AA3, first strand: chain 'A' and resid 106 through 108 Processing sheet with id=AA4, first strand: chain 'A' and resid 171 through 172 removed outlier: 4.039A pdb=" N VAL A 171 " --> pdb=" O ILE A 183 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 40 through 42 removed outlier: 3.674A pdb=" N ILE C 29 " --> pdb=" O GLU C 58 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASP C 56 " --> pdb=" O ARG C 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 176 through 177 removed outlier: 3.559A pdb=" N LEU C 176 " --> pdb=" O VAL C 291 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP C 293 " --> pdb=" O HIS C 283 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 219 through 224 Processing sheet with id=AA8, first strand: chain 'C' and resid 315 through 318 removed outlier: 3.515A pdb=" N ARG C 322 " --> pdb=" O SER C 318 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 27 through 30 removed outlier: 6.291A pdb=" N THR D 36 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE D 192 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 187 through 188 removed outlier: 6.164A pdb=" N SER D 227 " --> pdb=" O TYR D 14 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR D 14 " --> pdb=" O SER D 227 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D 5 " --> pdb=" O ALA D 287 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU D 283 " --> pdb=" O ILE D 9 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 336 " --> pdb=" O ILE D 286 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR E 36 " --> pdb=" O THR E 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 59 through 62 Processing sheet with id=AB5, first strand: chain 'E' and resid 200 through 207 Processing sheet with id=AB6, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.161A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 30 removed outlier: 6.161A pdb=" N THR F 36 " --> pdb=" O THR F 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 59 through 62 Processing sheet with id=AB9, first strand: chain 'F' and resid 200 through 206 Processing sheet with id=AC1, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR G 36 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR G 36 " --> pdb=" O THR G 193 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 59 through 62 Processing sheet with id=AC4, first strand: chain 'G' and resid 200 through 205 Processing sheet with id=AC5, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 27 through 30 removed outlier: 6.160A pdb=" N THR H 36 " --> pdb=" O THR H 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'H' and resid 59 through 62 Processing sheet with id=AC8, first strand: chain 'H' and resid 200 through 207 Processing sheet with id=AC9, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR I 36 " --> pdb=" O THR I 193 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 27 through 30 removed outlier: 6.162A pdb=" N THR I 36 " --> pdb=" O THR I 193 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLY I 229 " --> pdb=" O LEU I 12 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 59 through 62 Processing sheet with id=AD3, first strand: chain 'N' and resid 150 through 152 removed outlier: 5.274A pdb=" N VAL N 150 " --> pdb=" O ARG N 7 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG N 7 " --> pdb=" O VAL N 150 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG N 152 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL N 112 " --> pdb=" O ASP N 64 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG N 62 " --> pdb=" O THR N 114 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR N 60 " --> pdb=" O ALA N 116 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASP N 183 " --> pdb=" O VAL N 63 " (cutoff:3.500A) removed outlier: 8.926A pdb=" N ARG N 65 " --> pdb=" O LEU N 181 " (cutoff:3.500A) removed outlier: 13.805A pdb=" N LEU N 181 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ARG N 213 " --> pdb=" O PRO N 204 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N SER N 215 " --> pdb=" O ASP N 202 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU N 200 " --> pdb=" O ARG N 217 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'N' and resid 12 through 13 Processing sheet with id=AD5, first strand: chain 'N' and resid 12 through 13 1333 hydrogen bonds defined for protein. 3720 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 71 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 66 stacking parallelities Total time for adding SS restraints: 10.40 Time building geometry restraints manager: 12.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6173 1.32 - 1.45: 8270 1.45 - 1.58: 15021 1.58 - 1.71: 268 1.71 - 1.84: 80 Bond restraints: 29812 Sorted by residual: bond pdb=" C1' C K 55 " pdb=" N1 C K 55 " ideal model delta sigma weight residual 1.480 1.567 -0.087 1.50e-02 4.44e+03 3.35e+01 bond pdb=" C LEU I 12 " pdb=" N PRO I 13 " ideal model delta sigma weight residual 1.329 1.388 -0.059 1.20e-02 6.94e+03 2.43e+01 bond pdb=" C GLN C 84 " pdb=" N PRO C 85 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.18e-02 7.18e+03 2.38e+01 bond pdb=" C ARG C 130 " pdb=" N PRO C 131 " ideal model delta sigma weight residual 1.331 1.390 -0.060 1.31e-02 5.83e+03 2.08e+01 bond pdb=" C ASP C 256 " pdb=" N PRO C 257 " ideal model delta sigma weight residual 1.336 1.390 -0.054 1.20e-02 6.94e+03 2.00e+01 ... (remaining 29807 not shown) Histogram of bond angle deviations from ideal: 75.77 - 88.49: 1 88.49 - 101.21: 99 101.21 - 113.93: 18390 113.93 - 126.65: 21853 126.65 - 139.38: 777 Bond angle restraints: 41120 Sorted by residual: angle pdb=" C HIS A 185 " pdb=" N PRO A 186 " pdb=" CD PRO A 186 " ideal model delta sigma weight residual 125.00 75.77 49.23 4.10e+00 5.95e-02 1.44e+02 angle pdb=" N GLY C 166 " pdb=" CA GLY C 166 " pdb=" C GLY C 166 " ideal model delta sigma weight residual 112.68 97.58 15.10 1.26e+00 6.30e-01 1.44e+02 angle pdb=" N TRP C 163 " pdb=" CA TRP C 163 " pdb=" C TRP C 163 " ideal model delta sigma weight residual 111.28 123.18 -11.90 1.09e+00 8.42e-01 1.19e+02 angle pdb=" N ARG A 123 " pdb=" CA ARG A 123 " pdb=" C ARG A 123 " ideal model delta sigma weight residual 110.59 96.14 14.45 1.45e+00 4.76e-01 9.93e+01 angle pdb=" N ILE C 236 " pdb=" CA ILE C 236 " pdb=" C ILE C 236 " ideal model delta sigma weight residual 107.76 116.98 -9.22 1.01e+00 9.80e-01 8.33e+01 ... (remaining 41115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.17: 16770 32.17 - 64.34: 963 64.34 - 96.51: 52 96.51 - 128.68: 3 128.68 - 160.85: 3 Dihedral angle restraints: 17791 sinusoidal: 8136 harmonic: 9655 Sorted by residual: dihedral pdb=" O4' C K 55 " pdb=" C1' C K 55 " pdb=" N1 C K 55 " pdb=" C2 C K 55 " ideal model delta sinusoidal sigma weight residual 200.00 45.88 154.12 1 1.50e+01 4.44e-03 8.11e+01 dihedral pdb=" O4' U K 20 " pdb=" C1' U K 20 " pdb=" N1 U K 20 " pdb=" C2 U K 20 " ideal model delta sinusoidal sigma weight residual 200.00 82.12 117.88 1 1.50e+01 4.44e-03 6.26e+01 dihedral pdb=" N TYR A 164 " pdb=" C TYR A 164 " pdb=" CA TYR A 164 " pdb=" CB TYR A 164 " ideal model delta harmonic sigma weight residual 122.80 110.73 12.07 0 2.50e+00 1.60e-01 2.33e+01 ... (remaining 17788 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 4398 0.149 - 0.298: 234 0.298 - 0.448: 20 0.448 - 0.597: 2 0.597 - 0.746: 1 Chirality restraints: 4655 Sorted by residual: chirality pdb=" CG LEU N 138 " pdb=" CB LEU N 138 " pdb=" CD1 LEU N 138 " pdb=" CD2 LEU N 138 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CB THR D 193 " pdb=" CA THR D 193 " pdb=" OG1 THR D 193 " pdb=" CG2 THR D 193 " both_signs ideal model delta sigma weight residual False 2.55 1.99 0.56 2.00e-01 2.50e+01 7.91e+00 chirality pdb=" C1' DA M 50 " pdb=" O4' DA M 50 " pdb=" C2' DA M 50 " pdb=" N9 DA M 50 " both_signs ideal model delta sigma weight residual False 2.42 1.93 0.49 2.00e-01 2.50e+01 6.01e+00 ... (remaining 4652 not shown) Planarity restraints: 4869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 185 " -0.156 5.00e-02 4.00e+02 2.33e-01 8.66e+01 pdb=" N PRO A 186 " 0.398 5.00e-02 4.00e+02 pdb=" CA PRO A 186 " -0.167 5.00e-02 4.00e+02 pdb=" CD PRO A 186 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU C 427 " 0.034 2.00e-02 2.50e+03 6.90e-02 4.76e+01 pdb=" CD GLU C 427 " -0.119 2.00e-02 2.50e+03 pdb=" OE1 GLU C 427 " 0.042 2.00e-02 2.50e+03 pdb=" OE2 GLU C 427 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 390 " 0.006 2.00e-02 2.50e+03 3.67e-02 3.37e+01 pdb=" CG TRP C 390 " -0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP C 390 " 0.079 2.00e-02 2.50e+03 pdb=" CD2 TRP C 390 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP C 390 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TRP C 390 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP C 390 " 0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 390 " -0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 390 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP C 390 " 0.003 2.00e-02 2.50e+03 ... (remaining 4866 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.31: 94 2.31 - 2.96: 14742 2.96 - 3.61: 43232 3.61 - 4.25: 69502 4.25 - 4.90: 116165 Nonbonded interactions: 243735 Sorted by model distance: nonbonded pdb=" NE2 GLN A 122 " pdb=" N1 A K 44 " model vdw 1.667 3.200 nonbonded pdb=" OE1 GLN A 122 " pdb=" C5 A K 44 " model vdw 1.818 3.260 nonbonded pdb=" O ASP A 169 " pdb=" O ARG A 184 " model vdw 1.858 3.040 nonbonded pdb=" O GLN J 98 " pdb=" NE2 GLN J 98 " model vdw 1.876 3.120 nonbonded pdb=" NH2 ARG A 184 " pdb=" OP1 C K 46 " model vdw 1.926 3.120 ... (remaining 243730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'E' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = (chain 'F' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = (chain 'G' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = (chain 'H' and (resid 2 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 198 or resid 227 through 247 or (re \ sid 248 through 249 and (name N or name CA or name C or name O or name CB )) or \ resid 250 through 269 or resid 279 through 367)) selection = chain 'I' } ncs_group { reference = (chain 'J' and (resid 5 through 35 or resid 44 through 57 or resid 75 through 13 \ 5 or resid 137 through 215 or (resid 216 and (name N or name CA or name C or nam \ e O or name CB )) or resid 217 through 229)) selection = (chain 'L' and resid 5 through 229) } 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: 0.840 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: 0.040 Extract box with map and model: 1.030 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 79.830 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.150 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 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 0.151 29812 Z= 0.811 Angle : 1.365 49.234 41120 Z= 0.784 Chirality : 0.078 0.746 4655 Planarity : 0.008 0.233 4869 Dihedral : 17.115 160.852 11537 Min Nonbonded Distance : 1.667 Molprobity Statistics. All-atom Clashscore : 28.66 Ramachandran Plot: Outliers : 0.55 % Allowed : 4.65 % Favored : 94.80 % Rotamer: Outliers : 5.48 % Allowed : 6.64 % Favored : 87.88 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.12), residues: 3269 helix: -1.73 (0.11), residues: 1356 sheet: -2.28 (0.19), residues: 490 loop : -1.59 (0.14), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.006 TRP C 390 HIS 0.024 0.004 HIS H 216 PHE 0.080 0.004 PHE E 226 TYR 0.085 0.004 TYR C 315 ARG 0.036 0.001 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 876 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 730 time to evaluate : 3.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.1497 (mtt) cc_final: 0.0768 (mtm) REVERT: A 112 LYS cc_start: 0.3622 (OUTLIER) cc_final: 0.2391 (tttt) REVERT: C 51 SER cc_start: 0.8380 (OUTLIER) cc_final: 0.8114 (t) REVERT: C 106 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.5854 (ptm-80) REVERT: C 118 ASP cc_start: 0.8121 (OUTLIER) cc_final: 0.7702 (t0) REVERT: C 169 HIS cc_start: 0.6420 (OUTLIER) cc_final: 0.6187 (m90) REVERT: C 215 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8319 (pp) REVERT: C 336 ARG cc_start: 0.7108 (OUTLIER) cc_final: 0.6766 (ttt180) REVERT: C 343 HIS cc_start: 0.6462 (OUTLIER) cc_final: 0.4985 (t-90) REVERT: C 357 ASN cc_start: 0.7696 (m-40) cc_final: 0.7478 (m110) REVERT: C 424 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8647 (mmmt) REVERT: C 434 GLU cc_start: 0.6339 (pp20) cc_final: 0.5743 (pp20) REVERT: C 522 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7296 (mtm180) REVERT: D 20 ASP cc_start: 0.8280 (m-30) cc_final: 0.8009 (m-30) REVERT: D 50 GLU cc_start: 0.7879 (tp30) cc_final: 0.7602 (tp30) REVERT: D 341 GLU cc_start: 0.5122 (OUTLIER) cc_final: 0.4919 (pp20) REVERT: D 354 ASP cc_start: 0.7225 (m-30) cc_final: 0.6917 (p0) REVERT: E 148 LYS cc_start: 0.8241 (mttp) cc_final: 0.7471 (mmmm) REVERT: E 266 THR cc_start: 0.9017 (t) cc_final: 0.8733 (p) REVERT: F 5 ASP cc_start: 0.8052 (p0) cc_final: 0.7834 (p0) REVERT: F 22 LEU cc_start: 0.8488 (mt) cc_final: 0.8253 (mt) REVERT: F 113 THR cc_start: 0.8759 (p) cc_final: 0.8519 (t) REVERT: F 119 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8314 (pp) REVERT: G 154 ASP cc_start: 0.7811 (t0) cc_final: 0.7358 (t0) REVERT: G 221 MET cc_start: 0.8833 (mtp) cc_final: 0.8281 (mtp) REVERT: H 155 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7497 (mtp180) REVERT: H 208 ASP cc_start: 0.8262 (OUTLIER) cc_final: 0.7648 (m-30) REVERT: H 234 TYR cc_start: 0.8959 (t80) cc_final: 0.8624 (t80) REVERT: H 253 ARG cc_start: 0.7984 (ttt-90) cc_final: 0.6144 (mmt-90) REVERT: I 147 PRO cc_start: 0.7757 (Cg_endo) cc_final: 0.7479 (Cg_exo) REVERT: J 157 THR cc_start: 0.9367 (t) cc_final: 0.9032 (p) REVERT: J 211 ARG cc_start: 0.7214 (mmm160) cc_final: 0.6920 (mtp85) REVERT: L 8 GLN cc_start: 0.7226 (mt0) cc_final: 0.6751 (mt0) REVERT: L 18 SER cc_start: 0.7752 (t) cc_final: 0.7549 (p) REVERT: L 182 TYR cc_start: 0.8434 (t80) cc_final: 0.8224 (t80) REVERT: L 191 ASP cc_start: 0.8586 (t0) cc_final: 0.8300 (t0) REVERT: N 13 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8380 (pt0) REVERT: N 65 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7403 (ttp-170) REVERT: N 110 ASP cc_start: 0.6775 (t70) cc_final: 0.6373 (t70) REVERT: N 137 TYR cc_start: 0.8150 (p90) cc_final: 0.7901 (p90) REVERT: N 205 LEU cc_start: 0.8330 (mp) cc_final: 0.7899 (mp) REVERT: N 206 SER cc_start: 0.8069 (t) cc_final: 0.7485 (t) REVERT: N 244 THR cc_start: 0.8417 (m) cc_final: 0.8101 (p) outliers start: 146 outliers final: 48 residues processed: 835 average time/residue: 0.5066 time to fit residues: 615.7797 Evaluate side-chains 452 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 389 time to evaluate : 3.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ARG Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 106 ARG Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 119 TYR Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 177 ASP Chi-restraints excluded: chain C residue 185 LEU Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 334 ILE Chi-restraints excluded: chain C residue 335 TRP Chi-restraints excluded: chain C residue 336 ARG Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 424 LYS Chi-restraints excluded: chain C residue 494 THR Chi-restraints excluded: chain C residue 522 ARG Chi-restraints excluded: chain D residue 6 ILE Chi-restraints excluded: chain D residue 172 ARG Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain D residue 368 PHE Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 65 ILE Chi-restraints excluded: chain E residue 151 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 258 GLU Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 98 GLN Chi-restraints excluded: chain J residue 136 ARG Chi-restraints excluded: chain L residue 197 ARG Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 18 HIS Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain N residue 171 ARG Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 231 VAL Chi-restraints excluded: chain N residue 242 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 287 optimal weight: 0.9980 chunk 258 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 267 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 309 optimal weight: 9.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS C 100 GLN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN D 236 ASN E 18 ASN E 89 GLN E 134 HIS E 195 HIS F 18 ASN F 89 GLN F 195 HIS F 216 HIS F 222 ASN ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 HIS G 195 HIS ** G 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 ASN H 89 GLN ** H 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 HIS H 214 ASN H 225 GLN I 134 HIS L 145 GLN L 167 GLN L 173 HIS L 175 HIS L 208 HIS N 43 GLN ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29812 Z= 0.231 Angle : 0.700 21.022 41120 Z= 0.369 Chirality : 0.044 0.337 4655 Planarity : 0.006 0.179 4869 Dihedral : 19.091 156.510 5689 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.84 % Favored : 96.94 % Rotamer: Outliers : 4.28 % Allowed : 12.23 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.13), residues: 3269 helix: 0.01 (0.13), residues: 1364 sheet: -1.76 (0.20), residues: 482 loop : -1.14 (0.15), residues: 1423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP C 183 HIS 0.010 0.001 HIS A 150 PHE 0.029 0.002 PHE C 379 TYR 0.021 0.002 TYR I 321 ARG 0.008 0.001 ARG C 432 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 504 time to evaluate : 2.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.1212 (mtt) cc_final: 0.0546 (mtm) REVERT: C 97 ARG cc_start: 0.7385 (mtt180) cc_final: 0.7153 (mtt180) REVERT: C 118 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7764 (t0) REVERT: C 129 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.7296 (pp20) REVERT: C 169 HIS cc_start: 0.6438 (OUTLIER) cc_final: 0.6064 (m90) REVERT: C 343 HIS cc_start: 0.6590 (OUTLIER) cc_final: 0.5113 (t-90) REVERT: C 406 GLU cc_start: 0.6137 (OUTLIER) cc_final: 0.5170 (pm20) REVERT: C 434 GLU cc_start: 0.6708 (pp20) cc_final: 0.6465 (pp20) REVERT: C 438 LYS cc_start: 0.8838 (tttp) cc_final: 0.8345 (ttmt) REVERT: C 445 ASN cc_start: 0.7329 (m110) cc_final: 0.6425 (t0) REVERT: D 20 ASP cc_start: 0.8005 (m-30) cc_final: 0.7708 (m-30) REVERT: D 40 SER cc_start: 0.8618 (t) cc_final: 0.8292 (p) REVERT: D 269 SER cc_start: 0.8071 (p) cc_final: 0.7827 (m) REVERT: D 341 GLU cc_start: 0.6372 (OUTLIER) cc_final: 0.6155 (pm20) REVERT: D 354 ASP cc_start: 0.7404 (m-30) cc_final: 0.7090 (p0) REVERT: E 102 LEU cc_start: 0.9149 (mt) cc_final: 0.8934 (mt) REVERT: E 140 LYS cc_start: 0.8844 (mttm) cc_final: 0.8303 (mmtt) REVERT: E 148 LYS cc_start: 0.8151 (mttp) cc_final: 0.7725 (mmmm) REVERT: E 266 THR cc_start: 0.9044 (t) cc_final: 0.8748 (p) REVERT: E 312 LEU cc_start: 0.7894 (tp) cc_final: 0.7593 (tp) REVERT: E 363 MET cc_start: 0.8442 (mmt) cc_final: 0.7781 (mmt) REVERT: F 60 VAL cc_start: 0.8013 (t) cc_final: 0.7784 (p) REVERT: F 75 GLU cc_start: 0.7937 (pp20) cc_final: 0.7406 (tt0) REVERT: F 97 LYS cc_start: 0.6996 (mptt) cc_final: 0.6371 (ttpt) REVERT: F 113 THR cc_start: 0.8797 (p) cc_final: 0.8595 (t) REVERT: F 258 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7594 (tp30) REVERT: F 278 MET cc_start: 0.8636 (mmm) cc_final: 0.8041 (mmt) REVERT: F 301 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7768 (tm-30) REVERT: G 43 TRP cc_start: 0.9212 (OUTLIER) cc_final: 0.8457 (t-100) REVERT: G 50 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7394 (tp30) REVERT: G 101 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7803 (ttpt) REVERT: G 154 ASP cc_start: 0.7778 (t0) cc_final: 0.7433 (t0) REVERT: G 221 MET cc_start: 0.8729 (mtp) cc_final: 0.8193 (mtp) REVERT: G 227 SER cc_start: 0.9106 (t) cc_final: 0.8712 (m) REVERT: H 30 TYR cc_start: 0.9347 (t80) cc_final: 0.9118 (t80) REVERT: H 158 GLU cc_start: 0.7927 (tp30) cc_final: 0.7167 (pt0) REVERT: H 208 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7681 (m-30) REVERT: H 221 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8433 (ptp) REVERT: H 253 ARG cc_start: 0.8022 (ttt-90) cc_final: 0.6025 (mmt-90) REVERT: H 363 MET cc_start: 0.8961 (mmt) cc_final: 0.8135 (mmt) REVERT: I 250 GLN cc_start: 0.8078 (mm110) cc_final: 0.7577 (tp-100) REVERT: I 288 VAL cc_start: 0.7913 (t) cc_final: 0.7068 (m) REVERT: L 8 GLN cc_start: 0.7063 (mt0) cc_final: 0.6496 (mt0) REVERT: L 167 GLN cc_start: 0.8850 (mm-40) cc_final: 0.8635 (mm110) REVERT: L 226 ARG cc_start: 0.7509 (mmt-90) cc_final: 0.7225 (mmt-90) REVERT: N 13 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8843 (pt0) REVERT: N 65 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7726 (ttp-170) REVERT: N 69 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8108 (ttm110) REVERT: N 83 GLU cc_start: 0.7823 (mp0) cc_final: 0.7513 (mp0) REVERT: N 110 ASP cc_start: 0.6965 (t70) cc_final: 0.6213 (t70) REVERT: N 161 GLU cc_start: 0.8341 (tt0) cc_final: 0.8109 (tt0) REVERT: N 206 SER cc_start: 0.8116 (t) cc_final: 0.7564 (p) outliers start: 114 outliers final: 49 residues processed: 583 average time/residue: 0.4791 time to fit residues: 423.4135 Evaluate side-chains 429 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 365 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 59 ILE Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 169 HIS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 406 GLU Chi-restraints excluded: chain C residue 421 LEU Chi-restraints excluded: chain C residue 505 ASN Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain D residue 341 GLU Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 119 LEU Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 332 ASP Chi-restraints excluded: chain F residue 91 VAL Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 101 LYS Chi-restraints excluded: chain G residue 239 LEU Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain H residue 221 MET Chi-restraints excluded: chain I residue 21 ASP Chi-restraints excluded: chain I residue 43 TRP Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain I residue 251 THR Chi-restraints excluded: chain J residue 22 VAL Chi-restraints excluded: chain L residue 164 ILE Chi-restraints excluded: chain N residue 13 GLN Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 33 SER Chi-restraints excluded: chain N residue 65 ARG Chi-restraints excluded: chain N residue 69 ARG Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 242 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 172 optimal weight: 0.7980 chunk 96 optimal weight: 0.1980 chunk 257 optimal weight: 0.0000 chunk 210 optimal weight: 7.9990 chunk 85 optimal weight: 4.9990 chunk 310 optimal weight: 6.9990 chunk 335 optimal weight: 8.9990 chunk 276 optimal weight: 0.9980 chunk 307 optimal weight: 7.9990 chunk 105 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN ** C 184 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 502 ASN D 7 HIS E 89 GLN F 49 HIS ** G 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 225 GLN H 18 ASN H 49 HIS H 134 HIS H 225 GLN H 273 ASN J 9 HIS J 23 ASN J 91 GLN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29812 Z= 0.234 Angle : 0.623 13.681 41120 Z= 0.327 Chirality : 0.042 0.200 4655 Planarity : 0.005 0.153 4869 Dihedral : 18.640 155.862 5591 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.24 % Favored : 96.57 % Rotamer: Outliers : 3.98 % Allowed : 14.30 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % 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: -0.56 (0.14), residues: 3269 helix: 0.67 (0.14), residues: 1373 sheet: -1.44 (0.21), residues: 482 loop : -0.92 (0.15), residues: 1414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 390 HIS 0.009 0.001 HIS A 150 PHE 0.016 0.002 PHE L 81 TYR 0.017 0.002 TYR E 118 ARG 0.006 0.001 ARG D 289 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6538 Ramachandran restraints generated. 3269 Oldfield, 0 Emsley, 3269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 403 time to evaluate : 2.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 MET cc_start: 0.1119 (mtt) cc_final: 0.0775 (mtm) REVERT: C 46 ASP cc_start: 0.8241 (OUTLIER) cc_final: 0.7684 (t0) REVERT: C 76 THR cc_start: 0.7089 (OUTLIER) cc_final: 0.6678 (t) REVERT: C 97 ARG cc_start: 0.7307 (mtt180) cc_final: 0.7095 (mtt180) REVERT: C 118 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7973 (t0) REVERT: C 215 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8604 (pp) REVERT: C 343 HIS cc_start: 0.6614 (OUTLIER) cc_final: 0.5235 (t-90) REVERT: C 438 LYS cc_start: 0.8943 (tttp) cc_final: 0.8389 (ttmt) REVERT: C 445 ASN cc_start: 0.7262 (m110) cc_final: 0.6492 (t0) REVERT: C 478 GLU cc_start: 0.7308 (OUTLIER) cc_final: 0.7000 (tp30) REVERT: D 20 ASP cc_start: 0.7915 (m-30) cc_final: 0.7705 (m-30) REVERT: D 50 GLU cc_start: 0.8043 (tp30) cc_final: 0.7748 (tp30) REVERT: D 354 ASP cc_start: 0.7539 (m-30) cc_final: 0.7303 (p0) REVERT: E 148 LYS cc_start: 0.8100 (mttp) cc_final: 0.7687 (mmmm) REVERT: E 221 MET cc_start: 0.6908 (mtp) cc_final: 0.6320 (mtp) REVERT: E 222 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7204 (m110) REVERT: E 266 THR cc_start: 0.9149 (t) cc_final: 0.8888 (p) REVERT: E 316 GLN cc_start: 0.7711 (mt0) cc_final: 0.7196 (mt0) REVERT: E 361 ASP cc_start: 0.7119 (m-30) cc_final: 0.6879 (m-30) REVERT: E 363 MET cc_start: 0.8523 (mmt) cc_final: 0.8000 (mmt) REVERT: F 50 GLU cc_start: 0.7811 (tp30) cc_final: 0.7515 (tp30) REVERT: F 60 VAL cc_start: 0.8383 (t) cc_final: 0.8015 (p) REVERT: F 97 LYS cc_start: 0.7119 (mptt) cc_final: 0.6447 (ttpt) REVERT: F 113 THR cc_start: 0.8797 (p) cc_final: 0.8573 (t) REVERT: F 208 ASP cc_start: 0.8416 (OUTLIER) cc_final: 0.8087 (m-30) REVERT: F 258 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7952 (tp30) REVERT: F 278 MET cc_start: 0.8772 (mmm) cc_final: 0.8158 (mmt) REVERT: F 301 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7812 (tm-30) REVERT: G 43 TRP cc_start: 0.9226 (OUTLIER) cc_final: 0.8491 (t-100) REVERT: G 91 VAL cc_start: 0.8296 (t) cc_final: 0.7792 (m) REVERT: G 154 ASP cc_start: 0.7801 (t0) cc_final: 0.7468 (t0) REVERT: G 221 MET cc_start: 0.8667 (mtp) cc_final: 0.8190 (mtp) REVERT: H 119 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8931 (pp) REVERT: H 158 GLU cc_start: 0.7994 (tp30) cc_final: 0.7157 (pt0) REVERT: H 208 ASP cc_start: 0.8432 (OUTLIER) cc_final: 0.7693 (m-30) REVERT: H 253 ARG cc_start: 0.8323 (ttt-90) cc_final: 0.6032 (mmt-90) REVERT: I 188 PHE cc_start: 0.8643 (OUTLIER) cc_final: 0.7783 (t80) REVERT: I 193 THR cc_start: 0.8945 (OUTLIER) cc_final: 0.8592 (p) REVERT: I 250 GLN cc_start: 0.8103 (mm110) cc_final: 0.7652 (tp-100) REVERT: L 8 GLN cc_start: 0.7048 (mt0) cc_final: 0.6479 (mt0) REVERT: L 191 ASP cc_start: 0.8536 (t0) cc_final: 0.7943 (t0) REVERT: N 110 ASP cc_start: 0.7063 (t70) cc_final: 0.6602 (t0) REVERT: N 225 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7613 (mt-10) outliers start: 106 outliers final: 55 residues processed: 478 average time/residue: 0.4211 time to fit residues: 311.5422 Evaluate side-chains 421 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 352 time to evaluate : 3.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 138 TRP Chi-restraints excluded: chain C residue 46 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 118 ASP Chi-restraints excluded: chain C residue 129 GLU Chi-restraints excluded: chain C residue 200 ARG Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 256 ASP Chi-restraints excluded: chain C residue 342 LEU Chi-restraints excluded: chain C residue 343 HIS Chi-restraints excluded: chain C residue 350 TYR Chi-restraints excluded: chain C residue 363 GLN Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain C residue 372 LEU Chi-restraints excluded: chain C residue 478 GLU Chi-restraints excluded: chain C residue 535 THR Chi-restraints excluded: chain D residue 11 THR Chi-restraints excluded: chain D residue 166 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 188 PHE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 284 VAL Chi-restraints excluded: chain E residue 43 TRP Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain E residue 188 PHE Chi-restraints excluded: chain E residue 222 ASN Chi-restraints excluded: chain E residue 248 ASP Chi-restraints excluded: chain F residue 27 THR Chi-restraints excluded: chain F residue 94 VAL Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 208 ASP Chi-restraints excluded: chain F residue 212 LYS Chi-restraints excluded: chain F residue 258 GLU Chi-restraints excluded: chain F residue 265 SER Chi-restraints excluded: chain F residue 354 ASP Chi-restraints excluded: chain G residue 5 ASP Chi-restraints excluded: chain G residue 43 TRP Chi-restraints excluded: chain G residue 197 THR Chi-restraints excluded: chain G residue 225 GLN Chi-restraints excluded: chain G residue 280 LEU Chi-restraints excluded: chain G residue 341 GLU Chi-restraints excluded: chain H residue 11 THR Chi-restraints excluded: chain H residue 18 ASN Chi-restraints excluded: chain H residue 43 TRP Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 119 LEU Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 136 ASP Chi-restraints excluded: chain I residue 188 PHE Chi-restraints excluded: chain I residue 193 THR Chi-restraints excluded: chain L residue 227 GLN Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 TYR Chi-restraints excluded: chain N residue 52 ASP Chi-restraints excluded: chain N residue 71 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain N residue 199 VAL Chi-restraints excluded: chain N residue 200 LEU Chi-restraints excluded: chain N residue 215 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 306 optimal weight: 0.8980 chunk 233 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 148 optimal weight: 0.9980 chunk 208 optimal weight: 2.9990 chunk 311 optimal weight: 6.9990 chunk 329 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 295 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: