Starting phenix.real_space_refine (version: 1.21rc1) on Fri Apr 28 23:14:27 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/04_2023/5u0a_8478.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/04_2023/5u0a_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_8478/04_2023/5u0a_8478.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/04_2023/5u0a_8478.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/04_2023/5u0a_8478.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u0a_8478/04_2023/5u0a_8478.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/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: 15.53, per 1000 atoms: 0.54 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: 12.61 Conformation dependent library (CDL) restraints added in 3.8 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: 8.58 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: 10.20 Time building geometry restraints manager: 13.13 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: 16631 32.17 - 64.34: 835 64.34 - 96.51: 31 96.51 - 128.68: 3 128.68 - 160.85: 3 Dihedral angle restraints: 17503 sinusoidal: 7848 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 17500 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 2.600 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 2.520 nonbonded pdb=" NH2 ARG A 184 " pdb=" OP1 C K 46 " model vdw 1.926 2.520 ... (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 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: 1.220 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: 6.770 Check model and map are aligned: 0.480 Set scattering table: 0.250 Process input model: 81.040 Find NCS groups from input model: 1.450 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.080 ------------------------------------------------------------------------------- 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 : 16.044 160.852 11249 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 % 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 *********************** 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 : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 48 residues processed: 835 average time/residue: 0.5368 time to fit residues: 651.8581 Evaluate side-chains 432 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 384 time to evaluate : 3.593 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4265 time to fit residues: 36.4937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 287 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 138 optimal weight: 10.0000 chunk 267 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 162 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 309 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 ASN E 18 ASN E 89 GLN E 195 HIS F 18 ASN F 195 HIS F 216 HIS G 18 ASN G 134 HIS G 195 HIS ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN ** H 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 ASN ** H 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 134 HIS L 145 GLN L 167 GLN L 173 HIS L 175 HIS L 208 HIS L 218 HIS ** N 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.055 29812 Z= 0.228 Angle : 0.688 20.630 41120 Z= 0.362 Chirality : 0.043 0.268 4655 Planarity : 0.006 0.180 4869 Dihedral : 16.619 156.241 5239 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.91 % Favored : 96.88 % Rotamer Outliers : 3.15 % 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: -1.17 (0.13), residues: 3269 helix: 0.03 (0.13), residues: 1361 sheet: -1.72 (0.21), residues: 478 loop : -1.11 (0.15), residues: 1430 *********************** 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 578 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 494 time to evaluate : 3.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 84 outliers final: 41 residues processed: 549 average time/residue: 0.4802 time to fit residues: 401.9873 Evaluate side-chains 408 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 367 time to evaluate : 3.354 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.2800 time to fit residues: 25.9608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 172 optimal weight: 0.9990 chunk 96 optimal weight: 0.9990 chunk 257 optimal weight: 9.9990 chunk 210 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 310 optimal weight: 6.9990 chunk 335 optimal weight: 7.9990 chunk 276 optimal weight: 0.7980 chunk 307 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 248 optimal weight: 9.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS D 236 ASN G 18 ASN ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 273 ASN H 18 ASN H 49 HIS ** H 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 195 HIS H 225 GLN ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 9 HIS J 23 ASN ** N 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 29812 Z= 0.198 Angle : 0.602 13.209 41120 Z= 0.316 Chirality : 0.041 0.220 4655 Planarity : 0.005 0.151 4869 Dihedral : 16.377 156.242 5239 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.09 % Favored : 96.70 % Rotamer Outliers : 2.48 % 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: -0.51 (0.14), residues: 3269 helix: 0.69 (0.14), residues: 1379 sheet: -1.37 (0.21), residues: 494 loop : -0.89 (0.16), residues: 1396 *********************** 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 469 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 403 time to evaluate : 3.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 32 residues processed: 449 average time/residue: 0.4715 time to fit residues: 327.8998 Evaluate side-chains 371 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 339 time to evaluate : 3.235 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.3073 time to fit residues: 22.0743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 306 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 161 optimal weight: 0.0020 chunk 34 optimal weight: 20.0000 chunk 148 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 311 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 chunk 162 optimal weight: 0.7980 chunk 295 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 overall best weight: 2.1192 ------------------------------------------------------------------------------- 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 363 GLN ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 164 ASN H 18 ASN H 273 ASN I 195 HIS J 173 HIS L 227 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.093 29812 Z= 0.281 Angle : 0.622 10.322 41120 Z= 0.326 Chirality : 0.042 0.197 4655 Planarity : 0.005 0.134 4869 Dihedral : 16.306 158.532 5239 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.03 % Favored : 96.82 % Rotamer Outliers : 1.91 % 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: -0.29 (0.14), residues: 3269 helix: 0.90 (0.14), residues: 1386 sheet: -1.22 (0.21), residues: 482 loop : -0.84 (0.16), residues: 1401 *********************** REFINEMENT MACRO_CYCLE 4 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 423 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 372 time to evaluate : 3.561 Fit side-chains revert: symmetry clash outliers start: 51 outliers final: 23 residues processed: 404 average time/residue: 0.4617 time to fit residues: 285.9824 Evaluate side-chains 348 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 325 time to evaluate : 3.131 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.2560 time to fit residues: 15.1146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 274 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 245 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 281 optimal weight: 7.9990 chunk 227 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 168 optimal weight: 0.8980 chunk 295 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 HIS D 225 GLN D 236 ASN J 23 ASN J 175 HIS L 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 29812 Z= 0.215 Angle : 0.571 10.367 41120 Z= 0.298 Chirality : 0.040 0.185 4655 Planarity : 0.004 0.052 4869 Dihedral : 16.265 159.376 5239 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.88 % Rotamer Outliers : 1.54 % 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: -0.01 (0.14), residues: 3269 helix: 1.16 (0.14), residues: 1387 sheet: -1.07 (0.21), residues: 485 loop : -0.71 (0.16), residues: 1397 *********************** REFINEMENT MACRO_CYCLE 5 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 394 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 353 time to evaluate : 3.244 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 18 residues processed: 379 average time/residue: 0.4626 time to fit residues: 268.4393 Evaluate side-chains 336 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 318 time to evaluate : 3.320 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2920 time to fit residues: 13.9638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 110 optimal weight: 5.9990 chunk 296 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 193 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 329 optimal weight: 0.4980 chunk 273 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 109 optimal weight: 0.3980 chunk 173 optimal weight: 5.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- 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 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN H 285 HIS ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 49 HIS J 23 ASN J 175 HIS ** J 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 98 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.4669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 29812 Z= 0.210 Angle : 0.569 10.363 41120 Z= 0.296 Chirality : 0.040 0.182 4655 Planarity : 0.004 0.053 4869 Dihedral : 16.196 160.039 5239 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.06 % Favored : 96.82 % Rotamer Outliers : 1.46 % 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: 0.15 (0.15), residues: 3269 helix: 1.32 (0.14), residues: 1388 sheet: -1.00 (0.21), residues: 479 loop : -0.67 (0.16), residues: 1402 *********************** REFINEMENT MACRO_CYCLE 6 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 395 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 356 time to evaluate : 3.461 Fit side-chains outliers start: 39 outliers final: 17 residues processed: 382 average time/residue: 0.4701 time to fit residues: 277.9442 Evaluate side-chains 340 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 323 time to evaluate : 3.573 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.3116 time to fit residues: 14.0115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 318 optimal weight: 9.9990 chunk 37 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 240 optimal weight: 7.9990 chunk 186 optimal weight: 0.9980 chunk 277 optimal weight: 0.9990 chunk 184 optimal weight: 0.9990 chunk 328 optimal weight: 0.0370 chunk 205 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 151 optimal weight: 0.9990 overall best weight: 0.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN F 49 HIS I 89 GLN J 23 ASN J 175 HIS L 98 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.4887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 29812 Z= 0.170 Angle : 0.551 10.383 41120 Z= 0.286 Chirality : 0.039 0.215 4655 Planarity : 0.004 0.050 4869 Dihedral : 16.093 160.557 5239 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.09 % Favored : 96.79 % Rotamer Outliers : 1.39 % 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: 0.29 (0.15), residues: 3269 helix: 1.45 (0.14), residues: 1388 sheet: -0.88 (0.21), residues: 471 loop : -0.63 (0.16), residues: 1410 *********************** REFINEMENT MACRO_CYCLE 7 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 390 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 353 time to evaluate : 3.431 Fit side-chains outliers start: 37 outliers final: 19 residues processed: 376 average time/residue: 0.4554 time to fit residues: 267.7326 Evaluate side-chains 340 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 321 time to evaluate : 3.278 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3153 time to fit residues: 15.5787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 203 optimal weight: 0.7980 chunk 131 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 208 optimal weight: 6.9990 chunk 223 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 30 optimal weight: 8.9990 chunk 258 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 290 HIS ** C 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS D 225 GLN D 272 GLN ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 89 GLN J 23 ASN J 91 GLN J 227 GLN L 98 GLN L 153 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 29812 Z= 0.266 Angle : 0.592 10.348 41120 Z= 0.309 Chirality : 0.041 0.192 4655 Planarity : 0.005 0.062 4869 Dihedral : 16.027 160.872 5239 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.24 % Favored : 96.70 % Rotamer Outliers : 0.94 % 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: 0.20 (0.14), residues: 3269 helix: 1.42 (0.14), residues: 1382 sheet: -0.95 (0.22), residues: 479 loop : -0.70 (0.16), residues: 1408 *********************** REFINEMENT MACRO_CYCLE 8 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 350 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 325 time to evaluate : 3.124 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 13 residues processed: 341 average time/residue: 0.4566 time to fit residues: 242.7675 Evaluate side-chains 310 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 297 time to evaluate : 3.432 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3549 time to fit residues: 12.2695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 298 optimal weight: 3.9990 chunk 314 optimal weight: 5.9990 chunk 287 optimal weight: 0.8980 chunk 306 optimal weight: 9.9990 chunk 184 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 240 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 276 optimal weight: 1.9990 chunk 289 optimal weight: 7.9990 chunk 305 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 342 ASN ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN J 227 GLN L 98 GLN L 153 ASN L 227 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.5176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 29812 Z= 0.269 Angle : 0.600 11.305 41120 Z= 0.313 Chirality : 0.042 0.263 4655 Planarity : 0.005 0.055 4869 Dihedral : 16.005 161.408 5239 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.49 % Favored : 96.45 % Rotamer Outliers : 0.94 % 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: 0.13 (0.14), residues: 3269 helix: 1.38 (0.14), residues: 1381 sheet: -0.96 (0.21), residues: 479 loop : -0.78 (0.16), residues: 1409 *********************** REFINEMENT MACRO_CYCLE 9 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 325 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 300 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 316 average time/residue: 0.4799 time to fit residues: 240.2996 Evaluate side-chains 293 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 281 time to evaluate : 3.339 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.3031 time to fit residues: 11.2168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 201 optimal weight: 0.0030 chunk 323 optimal weight: 4.9990 chunk 197 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 225 optimal weight: 2.9990 chunk 339 optimal weight: 10.0000 chunk 312 optimal weight: 5.9990 chunk 270 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 208 optimal weight: 7.9990 chunk 165 optimal weight: 0.8980 overall best weight: 2.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 GLN D 272 GLN ** E 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 250 GLN J 23 ASN J 227 GLN L 98 GLN ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 227 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.5350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.060 29812 Z= 0.341 Angle : 0.640 10.449 41120 Z= 0.335 Chirality : 0.043 0.205 4655 Planarity : 0.005 0.077 4869 Dihedral : 16.020 161.903 5239 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.64 % Favored : 96.30 % Rotamer Outliers : 0.60 % 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: -0.07 (0.14), residues: 3269 helix: 1.21 (0.14), residues: 1382 sheet: -1.08 (0.22), residues: 457 loop : -0.89 (0.16), residues: 1430 ********************** REFINEMENT MACRO_CYCLE 10 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 318 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 302 time to evaluate : 3.390 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 313 average time/residue: 0.4681 time to fit residues: 227.1516 Evaluate side-chains 283 residues out of total 2703 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 276 time to evaluate : 3.446 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2763 time to fit residues: 8.0301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 341 random chunks: chunk 214 optimal weight: 0.8980 chunk 288 optimal weight: 8.9990 chunk 82 optimal weight: 0.8980 chunk 249 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 270 optimal weight: 0.0270 chunk 113 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 49 optimal weight: 0.5980 overall best weight: 0.8840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 23 ASN J 227 GLN L 98 GLN ** L 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.160080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.120669 restraints weight = 39588.906| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.80 r_work: 0.3218 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.5471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 29812 Z= 0.182 Angle : 0.582 12.816 41120 Z= 0.300 Chirality : 0.040 0.180 4655 Planarity : 0.004 0.060 4869 Dihedral : 15.958 161.921 5239 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.40 % Favored : 96.54 % Rotamer Outliers : 0.34 % 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: 0.14 (0.14), residues: 3269 helix: 1.38 (0.14), residues: 1390 sheet: -0.81 (0.21), residues: 476 loop : -0.84 (0.16), residues: 1403 =============================================================================== Job complete usr+sys time: 6744.02 seconds wall clock time: 122 minutes 41.58 seconds (7361.58 seconds total)