Starting phenix.real_space_refine on Thu Mar 14 08:11:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wco_32426/03_2024/7wco_32426.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wco_32426/03_2024/7wco_32426.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wco_32426/03_2024/7wco_32426.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wco_32426/03_2024/7wco_32426.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wco_32426/03_2024/7wco_32426.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wco_32426/03_2024/7wco_32426.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 5670 2.51 5 N 1585 2.21 5 O 1615 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "J ARG 412": "NH1" <-> "NH2" Residue "J ARG 437": "NH1" <-> "NH2" Residue "J ARG 438": "NH1" <-> "NH2" Residue "K TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 111": "NH1" <-> "NH2" Residue "L ARG 244": "NH1" <-> "NH2" Residue "L ARG 259": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 437": "NH1" <-> "NH2" Residue "A ARG 438": "NH1" <-> "NH2" Residue "B TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 111": "NH1" <-> "NH2" Residue "C ARG 244": "NH1" <-> "NH2" Residue "C ARG 259": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 437": "NH1" <-> "NH2" Residue "D ARG 438": "NH1" <-> "NH2" Residue "E TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 244": "NH1" <-> "NH2" Residue "F ARG 259": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G ARG 437": "NH1" <-> "NH2" Residue "G ARG 438": "NH1" <-> "NH2" Residue "H TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 111": "NH1" <-> "NH2" Residue "I ARG 244": "NH1" <-> "NH2" Residue "I ARG 259": "NH1" <-> "NH2" Residue "M ARG 412": "NH1" <-> "NH2" Residue "M ARG 437": "NH1" <-> "NH2" Residue "M ARG 438": "NH1" <-> "NH2" Residue "N TYR 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O ARG 244": "NH1" <-> "NH2" Residue "O ARG 259": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8950 Number of models: 1 Model: "" Number of chains: 15 Chain: "J" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 203 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "K" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 366 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "L" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1221 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "A" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 203 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 366 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "C" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1221 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "D" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 203 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 366 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "F" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1221 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "G" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 203 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 366 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "I" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1221 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 149} Chain: "M" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 203 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 366 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "O" Number of atoms: 1221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1221 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 149} Time building chain proxies: 4.82, per 1000 atoms: 0.54 Number of scatterers: 8950 At special positions: 0 Unit cell: (119.68, 116.96, 95.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 1615 8.00 N 1585 7.00 C 5670 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: 3.09 Conformation dependent library (CDL) restraints added in 1.7 seconds 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2150 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 33.9% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'J' and resid 412 through 435 removed outlier: 3.674A pdb=" N LEU J 417 " --> pdb=" O VAL J 413 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY J 418 " --> pdb=" O ALA J 414 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU J 422 " --> pdb=" O GLY J 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA J 423 " --> pdb=" O GLY J 419 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU J 430 " --> pdb=" O ALA J 426 " (cutoff:3.500A) Processing helix chain 'K' and resid 372 through 377 Processing helix chain 'K' and resid 377 through 382 Processing helix chain 'K' and resid 382 through 402 removed outlier: 3.831A pdb=" N PHE K 388 " --> pdb=" O SER K 384 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA K 391 " --> pdb=" O MET K 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS K 395 " --> pdb=" O ALA K 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU K 396 " --> pdb=" O ARG K 392 " (cutoff:3.500A) Proline residue: K 398 - end of helix removed outlier: 3.687A pdb=" N LEU K 401 " --> pdb=" O THR K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 407 through 414 removed outlier: 3.628A pdb=" N LEU K 411 " --> pdb=" O VAL K 407 " (cutoff:3.500A) Processing helix chain 'L' and resid 114 through 121 removed outlier: 3.554A pdb=" N GLU L 117 " --> pdb=" O MET L 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN L 118 " --> pdb=" O LYS L 115 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP L 119 " --> pdb=" O ILE L 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE L 121 " --> pdb=" O ASN L 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 182 removed outlier: 3.574A pdb=" N LYS L 179 " --> pdb=" O VAL L 176 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER L 180 " --> pdb=" O HIS L 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP L 181 " --> pdb=" O MET L 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA L 182 " --> pdb=" O LYS L 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 435 removed outlier: 3.674A pdb=" N LEU A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 422 " --> pdb=" O GLY A 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 423 " --> pdb=" O GLY A 419 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU A 430 " --> pdb=" O ALA A 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 382 through 402 removed outlier: 3.831A pdb=" N PHE B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 391 " --> pdb=" O MET B 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS B 395 " --> pdb=" O ALA B 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU B 396 " --> pdb=" O ARG B 392 " (cutoff:3.500A) Proline residue: B 398 - end of helix removed outlier: 3.687A pdb=" N LEU B 401 " --> pdb=" O THR B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 414 removed outlier: 3.628A pdb=" N LEU B 411 " --> pdb=" O VAL B 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 121 removed outlier: 3.553A pdb=" N GLU C 117 " --> pdb=" O MET C 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN C 118 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP C 119 " --> pdb=" O ILE C 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE C 121 " --> pdb=" O ASN C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 182 removed outlier: 3.574A pdb=" N LYS C 179 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER C 180 " --> pdb=" O HIS C 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP C 181 " --> pdb=" O MET C 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA C 182 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 435 removed outlier: 3.674A pdb=" N LEU D 417 " --> pdb=" O VAL D 413 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY D 418 " --> pdb=" O ALA D 414 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU D 422 " --> pdb=" O GLY D 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA D 423 " --> pdb=" O GLY D 419 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU D 430 " --> pdb=" O ALA D 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 377 Processing helix chain 'E' and resid 377 through 382 Processing helix chain 'E' and resid 382 through 402 removed outlier: 3.831A pdb=" N PHE E 388 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 391 " --> pdb=" O MET E 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS E 395 " --> pdb=" O ALA E 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU E 396 " --> pdb=" O ARG E 392 " (cutoff:3.500A) Proline residue: E 398 - end of helix removed outlier: 3.687A pdb=" N LEU E 401 " --> pdb=" O THR E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 407 through 414 removed outlier: 3.629A pdb=" N LEU E 411 " --> pdb=" O VAL E 407 " (cutoff:3.500A) Processing helix chain 'F' and resid 114 through 121 removed outlier: 3.553A pdb=" N GLU F 117 " --> pdb=" O MET F 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN F 118 " --> pdb=" O LYS F 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP F 119 " --> pdb=" O ILE F 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE F 121 " --> pdb=" O ASN F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 182 removed outlier: 3.574A pdb=" N LYS F 179 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER F 180 " --> pdb=" O HIS F 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP F 181 " --> pdb=" O MET F 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA F 182 " --> pdb=" O LYS F 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 435 removed outlier: 3.674A pdb=" N LEU G 417 " --> pdb=" O VAL G 413 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY G 418 " --> pdb=" O ALA G 414 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU G 422 " --> pdb=" O GLY G 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA G 423 " --> pdb=" O GLY G 419 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU G 430 " --> pdb=" O ALA G 426 " (cutoff:3.500A) Processing helix chain 'H' and resid 372 through 377 Processing helix chain 'H' and resid 377 through 382 Processing helix chain 'H' and resid 382 through 402 removed outlier: 3.831A pdb=" N PHE H 388 " --> pdb=" O SER H 384 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 391 " --> pdb=" O MET H 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS H 395 " --> pdb=" O ALA H 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU H 396 " --> pdb=" O ARG H 392 " (cutoff:3.500A) Proline residue: H 398 - end of helix removed outlier: 3.687A pdb=" N LEU H 401 " --> pdb=" O THR H 397 " (cutoff:3.500A) Processing helix chain 'H' and resid 407 through 414 removed outlier: 3.629A pdb=" N LEU H 411 " --> pdb=" O VAL H 407 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 121 removed outlier: 3.554A pdb=" N GLU I 117 " --> pdb=" O MET I 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN I 118 " --> pdb=" O LYS I 115 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP I 119 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE I 121 " --> pdb=" O ASN I 118 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 182 removed outlier: 3.574A pdb=" N LYS I 179 " --> pdb=" O VAL I 176 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N SER I 180 " --> pdb=" O HIS I 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP I 181 " --> pdb=" O MET I 178 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA I 182 " --> pdb=" O LYS I 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 412 through 435 removed outlier: 3.674A pdb=" N LEU M 417 " --> pdb=" O VAL M 413 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY M 418 " --> pdb=" O ALA M 414 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU M 422 " --> pdb=" O GLY M 418 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA M 423 " --> pdb=" O GLY M 419 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU M 430 " --> pdb=" O ALA M 426 " (cutoff:3.500A) Processing helix chain 'N' and resid 372 through 377 Processing helix chain 'N' and resid 377 through 382 Processing helix chain 'N' and resid 382 through 402 removed outlier: 3.831A pdb=" N PHE N 388 " --> pdb=" O SER N 384 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA N 391 " --> pdb=" O MET N 387 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N CYS N 395 " --> pdb=" O ALA N 391 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU N 396 " --> pdb=" O ARG N 392 " (cutoff:3.500A) Proline residue: N 398 - end of helix removed outlier: 3.687A pdb=" N LEU N 401 " --> pdb=" O THR N 397 " (cutoff:3.500A) Processing helix chain 'N' and resid 407 through 414 removed outlier: 3.628A pdb=" N LEU N 411 " --> pdb=" O VAL N 407 " (cutoff:3.500A) Processing helix chain 'O' and resid 114 through 121 removed outlier: 3.554A pdb=" N GLU O 117 " --> pdb=" O MET O 114 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ASN O 118 " --> pdb=" O LYS O 115 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP O 119 " --> pdb=" O ILE O 116 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE O 121 " --> pdb=" O ASN O 118 " (cutoff:3.500A) Processing helix chain 'O' and resid 175 through 182 removed outlier: 3.574A pdb=" N LYS O 179 " --> pdb=" O VAL O 176 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N SER O 180 " --> pdb=" O HIS O 177 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP O 181 " --> pdb=" O MET O 178 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ALA O 182 " --> pdb=" O LYS O 179 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'L' and resid 130 through 133 removed outlier: 7.196A pdb=" N VAL L 124 " --> pdb=" O THR L 131 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'L' and resid 184 through 185 removed outlier: 6.710A pdb=" N LYS L 184 " --> pdb=" O VAL L 231 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA L 233 " --> pdb=" O LYS L 184 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE L 224 " --> pdb=" O VAL L 232 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'L' and resid 193 through 194 removed outlier: 3.670A pdb=" N GLN L 202 " --> pdb=" O THR L 209 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'L' and resid 249 through 252 removed outlier: 3.530A pdb=" N THR L 251 " --> pdb=" O THR L 258 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 130 through 133 removed outlier: 7.195A pdb=" N VAL C 124 " --> pdb=" O THR C 131 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 184 through 185 removed outlier: 6.710A pdb=" N LYS C 184 " --> pdb=" O VAL C 231 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA C 233 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE C 224 " --> pdb=" O VAL C 232 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 193 through 194 removed outlier: 3.671A pdb=" N GLN C 202 " --> pdb=" O THR C 209 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 249 through 252 removed outlier: 3.530A pdb=" N THR C 251 " --> pdb=" O THR C 258 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 130 through 133 removed outlier: 7.196A pdb=" N VAL F 124 " --> pdb=" O THR F 131 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 184 through 185 removed outlier: 6.710A pdb=" N LYS F 184 " --> pdb=" O VAL F 231 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N ALA F 233 " --> pdb=" O LYS F 184 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE F 224 " --> pdb=" O VAL F 232 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 193 through 194 removed outlier: 3.670A pdb=" N GLN F 202 " --> pdb=" O THR F 209 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'F' and resid 249 through 252 removed outlier: 3.530A pdb=" N THR F 251 " --> pdb=" O THR F 258 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 130 through 133 removed outlier: 7.196A pdb=" N VAL I 124 " --> pdb=" O THR I 131 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 184 through 185 removed outlier: 6.710A pdb=" N LYS I 184 " --> pdb=" O VAL I 231 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA I 233 " --> pdb=" O LYS I 184 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE I 224 " --> pdb=" O VAL I 232 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'I' and resid 193 through 194 removed outlier: 3.670A pdb=" N GLN I 202 " --> pdb=" O THR I 209 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'I' and resid 249 through 252 removed outlier: 3.530A pdb=" N THR I 251 " --> pdb=" O THR I 258 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'O' and resid 130 through 133 removed outlier: 7.196A pdb=" N VAL O 124 " --> pdb=" O THR O 131 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'O' and resid 184 through 185 removed outlier: 6.710A pdb=" N LYS O 184 " --> pdb=" O VAL O 231 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N ALA O 233 " --> pdb=" O LYS O 184 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE O 224 " --> pdb=" O VAL O 232 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'O' and resid 193 through 194 removed outlier: 3.670A pdb=" N GLN O 202 " --> pdb=" O THR O 209 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'O' and resid 249 through 252 removed outlier: 3.530A pdb=" N THR O 251 " --> pdb=" O THR O 258 " (cutoff:3.500A) 235 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.10 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2875 1.34 - 1.46: 1979 1.46 - 1.58: 4156 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 9125 Sorted by residual: bond pdb=" N ALA H 420 " pdb=" CA ALA H 420 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.21e+00 bond pdb=" N ALA B 420 " pdb=" CA ALA B 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 6.06e+00 bond pdb=" N ALA K 420 " pdb=" CA ALA K 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 6.01e+00 bond pdb=" N ALA E 420 " pdb=" CA ALA E 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.91e+00 bond pdb=" N ALA N 420 " pdb=" CA ALA N 420 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.27e-02 6.20e+03 5.88e+00 ... (remaining 9120 not shown) Histogram of bond angle deviations from ideal: 99.78 - 106.83: 355 106.83 - 113.88: 5190 113.88 - 120.93: 4048 120.93 - 127.98: 2688 127.98 - 135.03: 84 Bond angle restraints: 12365 Sorted by residual: angle pdb=" CA LYS F 158 " pdb=" CB LYS F 158 " pdb=" CG LYS F 158 " ideal model delta sigma weight residual 114.10 122.60 -8.50 2.00e+00 2.50e-01 1.81e+01 angle pdb=" CA LYS C 158 " pdb=" CB LYS C 158 " pdb=" CG LYS C 158 " ideal model delta sigma weight residual 114.10 122.60 -8.50 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA LYS L 158 " pdb=" CB LYS L 158 " pdb=" CG LYS L 158 " ideal model delta sigma weight residual 114.10 122.60 -8.50 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA LYS O 158 " pdb=" CB LYS O 158 " pdb=" CG LYS O 158 " ideal model delta sigma weight residual 114.10 122.59 -8.49 2.00e+00 2.50e-01 1.80e+01 angle pdb=" CA LYS I 158 " pdb=" CB LYS I 158 " pdb=" CG LYS I 158 " ideal model delta sigma weight residual 114.10 122.56 -8.46 2.00e+00 2.50e-01 1.79e+01 ... (remaining 12360 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 5185 17.01 - 34.03: 195 34.03 - 51.04: 75 51.04 - 68.05: 0 68.05 - 85.06: 5 Dihedral angle restraints: 5460 sinusoidal: 2085 harmonic: 3375 Sorted by residual: dihedral pdb=" CA ARG H 419 " pdb=" C ARG H 419 " pdb=" N ALA H 420 " pdb=" CA ALA H 420 " ideal model delta harmonic sigma weight residual 180.00 131.29 48.71 0 5.00e+00 4.00e-02 9.49e+01 dihedral pdb=" CA ARG K 419 " pdb=" C ARG K 419 " pdb=" N ALA K 420 " pdb=" CA ALA K 420 " ideal model delta harmonic sigma weight residual 180.00 131.31 48.69 0 5.00e+00 4.00e-02 9.48e+01 dihedral pdb=" CA ARG B 419 " pdb=" C ARG B 419 " pdb=" N ALA B 420 " pdb=" CA ALA B 420 " ideal model delta harmonic sigma weight residual 180.00 131.31 48.69 0 5.00e+00 4.00e-02 9.48e+01 ... (remaining 5457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 953 0.054 - 0.108: 368 0.108 - 0.162: 88 0.162 - 0.216: 16 0.216 - 0.270: 10 Chirality restraints: 1435 Sorted by residual: chirality pdb=" CA THR B 397 " pdb=" N THR B 397 " pdb=" C THR B 397 " pdb=" CB THR B 397 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" CA THR N 397 " pdb=" N THR N 397 " pdb=" C THR N 397 " pdb=" CB THR N 397 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA THR H 397 " pdb=" N THR H 397 " pdb=" C THR H 397 " pdb=" CB THR H 397 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1432 not shown) Planarity restraints: 1555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR G 435 " -0.030 2.00e-02 2.50e+03 5.80e-02 3.36e+01 pdb=" C THR G 435 " 0.100 2.00e-02 2.50e+03 pdb=" O THR G 435 " -0.037 2.00e-02 2.50e+03 pdb=" N MET G 436 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 435 " -0.030 2.00e-02 2.50e+03 5.80e-02 3.36e+01 pdb=" C THR D 435 " 0.100 2.00e-02 2.50e+03 pdb=" O THR D 435 " -0.037 2.00e-02 2.50e+03 pdb=" N MET D 436 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR J 435 " -0.030 2.00e-02 2.50e+03 5.79e-02 3.35e+01 pdb=" C THR J 435 " 0.100 2.00e-02 2.50e+03 pdb=" O THR J 435 " -0.037 2.00e-02 2.50e+03 pdb=" N MET J 436 " -0.033 2.00e-02 2.50e+03 ... (remaining 1552 not shown) Histogram of nonbonded interaction distances: 0.60 - 1.46: 45 1.46 - 2.32: 80 2.32 - 3.18: 7375 3.18 - 4.04: 20489 4.04 - 4.90: 36824 Warning: very small nonbonded interaction distances. Nonbonded interactions: 64813 Sorted by model distance: nonbonded pdb=" CD1 LEU H 411 " pdb=" CZ ARG M 437 " model vdw 0.599 3.690 nonbonded pdb=" CD1 LEU B 411 " pdb=" CZ ARG D 437 " model vdw 0.600 3.690 nonbonded pdb=" CD1 LEU K 411 " pdb=" CZ ARG A 437 " model vdw 0.600 3.690 nonbonded pdb=" CZ ARG J 437 " pdb=" CD1 LEU N 411 " model vdw 0.600 3.690 nonbonded pdb=" CD1 LEU E 411 " pdb=" CZ ARG G 437 " model vdw 0.600 3.690 ... (remaining 64808 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' selection = chain 'O' } 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 group one per residue 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: 1.420 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: 0.010 Extract box with map and model: 7.500 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 25.550 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.090 9125 Z= 0.544 Angle : 1.133 10.027 12365 Z= 0.617 Chirality : 0.063 0.270 1435 Planarity : 0.011 0.082 1555 Dihedral : 11.024 85.063 3310 Min Nonbonded Distance : 0.599 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.16 % Favored : 85.84 % Rotamer: Outliers : 0.53 % Allowed : 7.41 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.89 % 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: -5.43 (0.18), residues: 1165 helix: -4.70 (0.11), residues: 300 sheet: -3.60 (0.36), residues: 120 loop : -3.29 (0.19), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP C 196 HIS 0.009 0.002 HIS F 146 PHE 0.012 0.002 PHE C 208 TYR 0.025 0.003 TYR I 161 ARG 0.003 0.001 ARG C 259 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 357 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7698 (mtt180) cc_final: 0.6632 (mtm-85) REVERT: K 387 MET cc_start: 0.8317 (mtt) cc_final: 0.8109 (mtp) REVERT: K 394 LYS cc_start: 0.9341 (ttmt) cc_final: 0.8945 (ttmm) REVERT: K 415 CYS cc_start: 0.8340 (m) cc_final: 0.8100 (m) REVERT: L 126 LEU cc_start: 0.8053 (pt) cc_final: 0.7846 (tp) REVERT: L 235 VAL cc_start: 0.9695 (t) cc_final: 0.9457 (p) REVERT: A 412 ARG cc_start: 0.7635 (mtt180) cc_final: 0.6776 (mtm-85) REVERT: B 387 MET cc_start: 0.8243 (mtt) cc_final: 0.8029 (mtp) REVERT: B 394 LYS cc_start: 0.9361 (ttmt) cc_final: 0.9000 (ttmm) REVERT: C 133 TYR cc_start: 0.8833 (m-80) cc_final: 0.8623 (m-80) REVERT: C 135 CYS cc_start: 0.8901 (t) cc_final: 0.8645 (t) REVERT: C 168 ASP cc_start: 0.8756 (t70) cc_final: 0.8300 (t0) REVERT: C 235 VAL cc_start: 0.9734 (t) cc_final: 0.9480 (p) REVERT: D 412 ARG cc_start: 0.7586 (mtt180) cc_final: 0.6356 (mtm-85) REVERT: E 394 LYS cc_start: 0.9418 (ttmt) cc_final: 0.9048 (ttmm) REVERT: F 112 MET cc_start: 0.7627 (ttm) cc_final: 0.7304 (mmm) REVERT: F 202 GLN cc_start: 0.8636 (pm20) cc_final: 0.8434 (pt0) REVERT: F 235 VAL cc_start: 0.9736 (t) cc_final: 0.9500 (p) REVERT: F 265 THR cc_start: 0.8921 (p) cc_final: 0.8562 (t) REVERT: F 266 GLU cc_start: 0.8000 (pm20) cc_final: 0.7653 (pm20) REVERT: G 412 ARG cc_start: 0.7570 (mtt180) cc_final: 0.6473 (mtm-85) REVERT: H 386 TYR cc_start: 0.9010 (t80) cc_final: 0.8602 (t80) REVERT: H 387 MET cc_start: 0.8312 (mtt) cc_final: 0.8080 (mtp) REVERT: H 394 LYS cc_start: 0.9420 (ttmt) cc_final: 0.9029 (ttmm) REVERT: I 136 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8764 (tt) REVERT: I 161 TYR cc_start: 0.7971 (p90) cc_final: 0.7566 (p90) REVERT: I 168 ASP cc_start: 0.8841 (t70) cc_final: 0.8630 (t0) REVERT: I 185 TYR cc_start: 0.9202 (p90) cc_final: 0.8962 (p90) REVERT: I 266 GLU cc_start: 0.7898 (pm20) cc_final: 0.7398 (pm20) REVERT: M 412 ARG cc_start: 0.7641 (mtt180) cc_final: 0.7022 (mpp-170) REVERT: N 386 TYR cc_start: 0.9146 (t80) cc_final: 0.8713 (t80) REVERT: N 388 PHE cc_start: 0.8612 (m-10) cc_final: 0.8406 (m-10) REVERT: N 394 LYS cc_start: 0.9285 (ttmt) cc_final: 0.9046 (ttmm) REVERT: N 415 CYS cc_start: 0.7679 (m) cc_final: 0.7440 (m) REVERT: O 112 MET cc_start: 0.7646 (ttm) cc_final: 0.7117 (mmm) REVERT: O 133 TYR cc_start: 0.8830 (m-80) cc_final: 0.8614 (m-80) REVERT: O 136 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8659 (tt) REVERT: O 142 MET cc_start: 0.8781 (mtt) cc_final: 0.8560 (mtt) REVERT: O 161 TYR cc_start: 0.8101 (p90) cc_final: 0.7640 (p90) REVERT: O 204 SER cc_start: 0.9172 (t) cc_final: 0.8621 (p) REVERT: O 266 GLU cc_start: 0.7870 (pm20) cc_final: 0.7581 (pm20) outliers start: 5 outliers final: 0 residues processed: 362 average time/residue: 0.2244 time to fit residues: 107.5346 Evaluate side-chains 298 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 296 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 136 LEU Chi-restraints excluded: chain O residue 136 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 46 optimal weight: 7.9990 chunk 28 optimal weight: 0.4980 chunk 56 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 99 optimal weight: 0.7980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 202 GLN C 193 HIS C 202 GLN F 202 GLN I 202 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9125 Z= 0.232 Angle : 0.685 8.181 12365 Z= 0.361 Chirality : 0.046 0.189 1435 Planarity : 0.009 0.084 1555 Dihedral : 8.120 85.088 1294 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.53 % Favored : 90.47 % Rotamer: Outliers : 4.66 % Allowed : 16.83 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.20), residues: 1165 helix: -3.30 (0.19), residues: 320 sheet: -3.29 (0.41), residues: 120 loop : -3.22 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 196 HIS 0.004 0.001 HIS C 193 PHE 0.008 0.001 PHE E 388 TYR 0.022 0.002 TYR I 133 ARG 0.025 0.001 ARG M 437 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 335 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7453 (mtt180) cc_final: 0.6677 (mpp-170) REVERT: K 387 MET cc_start: 0.8367 (mtt) cc_final: 0.8012 (mtp) REVERT: K 394 LYS cc_start: 0.9319 (ttmt) cc_final: 0.8807 (ttmm) REVERT: L 112 MET cc_start: 0.7674 (ttm) cc_final: 0.7361 (tpt) REVERT: L 142 MET cc_start: 0.8627 (mtt) cc_final: 0.8388 (mtp) REVERT: L 204 SER cc_start: 0.9276 (t) cc_final: 0.8570 (p) REVERT: L 207 ARG cc_start: 0.8789 (ptm160) cc_final: 0.8491 (mtp-110) REVERT: L 235 VAL cc_start: 0.9712 (t) cc_final: 0.9470 (p) REVERT: A 412 ARG cc_start: 0.7611 (mtt180) cc_final: 0.6887 (mpp-170) REVERT: B 387 MET cc_start: 0.8235 (mtt) cc_final: 0.7910 (mtp) REVERT: B 394 LYS cc_start: 0.9344 (ttmt) cc_final: 0.8896 (ttmm) REVERT: C 112 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7332 (tpp) REVERT: C 133 TYR cc_start: 0.8847 (m-80) cc_final: 0.8541 (m-10) REVERT: C 136 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8635 (tt) REVERT: C 168 ASP cc_start: 0.8842 (t70) cc_final: 0.8585 (t70) REVERT: D 412 ARG cc_start: 0.7547 (mtt180) cc_final: 0.6601 (mpp-170) REVERT: E 394 LYS cc_start: 0.9420 (ttmt) cc_final: 0.8962 (ttmm) REVERT: F 112 MET cc_start: 0.7684 (ttm) cc_final: 0.7402 (tpp) REVERT: F 153 ASN cc_start: 0.9157 (t0) cc_final: 0.8792 (t0) REVERT: F 156 LEU cc_start: 0.8504 (mp) cc_final: 0.8118 (mt) REVERT: F 168 ASP cc_start: 0.8758 (t70) cc_final: 0.8365 (t70) REVERT: F 204 SER cc_start: 0.9115 (t) cc_final: 0.8422 (p) REVERT: F 240 ASN cc_start: 0.9267 (t0) cc_final: 0.9022 (t0) REVERT: F 265 THR cc_start: 0.8928 (p) cc_final: 0.8577 (t) REVERT: F 266 GLU cc_start: 0.7981 (pm20) cc_final: 0.7659 (pm20) REVERT: G 412 ARG cc_start: 0.7663 (mtt180) cc_final: 0.6889 (mpp-170) REVERT: H 386 TYR cc_start: 0.8782 (t80) cc_final: 0.8418 (t80) REVERT: H 387 MET cc_start: 0.8379 (mtt) cc_final: 0.8164 (mtp) REVERT: H 394 LYS cc_start: 0.9321 (ttmt) cc_final: 0.8956 (ttmm) REVERT: I 152 ASP cc_start: 0.8209 (t0) cc_final: 0.7966 (t0) REVERT: I 185 TYR cc_start: 0.9196 (p90) cc_final: 0.8940 (p90) REVERT: I 204 SER cc_start: 0.9255 (t) cc_final: 0.8645 (p) REVERT: I 266 GLU cc_start: 0.7791 (pm20) cc_final: 0.7480 (pm20) REVERT: M 412 ARG cc_start: 0.7501 (mtt180) cc_final: 0.6792 (mpp-170) REVERT: N 394 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9005 (ttmm) REVERT: O 112 MET cc_start: 0.7398 (ttm) cc_final: 0.7075 (mmm) REVERT: O 133 TYR cc_start: 0.8932 (m-80) cc_final: 0.8731 (m-80) REVERT: O 204 SER cc_start: 0.9131 (t) cc_final: 0.8508 (p) REVERT: O 266 GLU cc_start: 0.7805 (pm20) cc_final: 0.7526 (pm20) REVERT: O 268 TRP cc_start: 0.8805 (m-10) cc_final: 0.8391 (m-10) outliers start: 44 outliers final: 24 residues processed: 354 average time/residue: 0.2229 time to fit residues: 104.6164 Evaluate side-chains 331 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 305 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain J residue 437 ARG Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 437 ARG Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 437 ARG Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 437 ARG Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 20.0000 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 68 optimal weight: 0.0040 chunk 27 optimal weight: 0.0970 chunk 100 optimal weight: 0.0980 chunk 108 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.4980 chunk 80 optimal weight: 10.0000 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9125 Z= 0.158 Angle : 0.598 7.266 12365 Z= 0.305 Chirality : 0.043 0.157 1435 Planarity : 0.007 0.058 1555 Dihedral : 7.338 89.990 1292 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 4.44 % Allowed : 18.84 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.12 (0.20), residues: 1165 helix: -2.37 (0.23), residues: 335 sheet: -3.32 (0.38), residues: 120 loop : -2.94 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP L 196 HIS 0.003 0.001 HIS L 146 PHE 0.009 0.001 PHE N 388 TYR 0.021 0.002 TYR N 386 ARG 0.006 0.000 ARG B 393 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 334 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7343 (mtt180) cc_final: 0.6631 (mpp-170) REVERT: K 394 LYS cc_start: 0.9405 (ttmt) cc_final: 0.8978 (ttmm) REVERT: L 175 PRO cc_start: 0.9337 (Cg_exo) cc_final: 0.9057 (Cg_endo) REVERT: L 204 SER cc_start: 0.9210 (t) cc_final: 0.8476 (p) REVERT: B 387 MET cc_start: 0.8118 (mtt) cc_final: 0.7892 (mtp) REVERT: B 394 LYS cc_start: 0.9302 (ttmt) cc_final: 0.8845 (ttmm) REVERT: C 112 MET cc_start: 0.7636 (ttp) cc_final: 0.7392 (tpp) REVERT: C 168 ASP cc_start: 0.8775 (t70) cc_final: 0.8255 (t70) REVERT: C 265 THR cc_start: 0.8805 (p) cc_final: 0.8166 (t) REVERT: C 268 TRP cc_start: 0.8656 (m-10) cc_final: 0.8393 (m-10) REVERT: D 412 ARG cc_start: 0.7551 (mtt180) cc_final: 0.6679 (mpp-170) REVERT: E 394 LYS cc_start: 0.9367 (ttmt) cc_final: 0.8907 (ttmm) REVERT: F 156 LEU cc_start: 0.8346 (mp) cc_final: 0.7926 (mp) REVERT: F 168 ASP cc_start: 0.8840 (t70) cc_final: 0.8438 (t70) REVERT: F 189 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8667 (pttm) REVERT: F 204 SER cc_start: 0.8728 (t) cc_final: 0.7980 (p) REVERT: F 216 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.9080 (ttmm) REVERT: F 265 THR cc_start: 0.8773 (p) cc_final: 0.8338 (t) REVERT: G 412 ARG cc_start: 0.7454 (mtt180) cc_final: 0.6883 (mpp-170) REVERT: H 386 TYR cc_start: 0.8627 (t80) cc_final: 0.8247 (t80) REVERT: H 394 LYS cc_start: 0.9226 (ttmt) cc_final: 0.8915 (ttmm) REVERT: I 112 MET cc_start: 0.7877 (ttm) cc_final: 0.7446 (tpt) REVERT: I 152 ASP cc_start: 0.8236 (t0) cc_final: 0.8006 (t0) REVERT: I 175 PRO cc_start: 0.9384 (Cg_exo) cc_final: 0.9065 (Cg_endo) REVERT: I 185 TYR cc_start: 0.9230 (p90) cc_final: 0.8992 (p90) REVERT: I 204 SER cc_start: 0.9054 (t) cc_final: 0.8473 (p) REVERT: I 266 GLU cc_start: 0.7711 (pm20) cc_final: 0.7407 (pm20) REVERT: M 436 MET cc_start: 0.8294 (tmm) cc_final: 0.8008 (tmm) REVERT: N 388 PHE cc_start: 0.8279 (m-10) cc_final: 0.8033 (m-10) REVERT: N 394 LYS cc_start: 0.9365 (ttmt) cc_final: 0.9099 (ttmm) REVERT: O 133 TYR cc_start: 0.8707 (m-80) cc_final: 0.8318 (m-80) REVERT: O 156 LEU cc_start: 0.8241 (mp) cc_final: 0.7706 (mp) REVERT: O 175 PRO cc_start: 0.9423 (Cg_exo) cc_final: 0.8890 (Cg_endo) REVERT: O 204 SER cc_start: 0.9003 (t) cc_final: 0.8365 (p) REVERT: O 240 ASN cc_start: 0.9190 (t0) cc_final: 0.8938 (t0) REVERT: O 265 THR cc_start: 0.8889 (p) cc_final: 0.8253 (t) REVERT: O 266 GLU cc_start: 0.7690 (pm20) cc_final: 0.7335 (pm20) REVERT: O 268 TRP cc_start: 0.8695 (m-10) cc_final: 0.8211 (m-10) outliers start: 42 outliers final: 25 residues processed: 366 average time/residue: 0.2231 time to fit residues: 107.4825 Evaluate side-chains 323 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 296 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 188 GLU Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 216 LYS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 11 optimal weight: 0.0980 chunk 47 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 7.9990 chunk 106 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9125 Z= 0.263 Angle : 0.653 9.910 12365 Z= 0.330 Chirality : 0.045 0.157 1435 Planarity : 0.006 0.057 1555 Dihedral : 7.114 84.965 1292 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 6.77 % Allowed : 23.49 % Favored : 69.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.21), residues: 1165 helix: -1.68 (0.27), residues: 320 sheet: -3.34 (0.38), residues: 120 loop : -3.01 (0.20), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 196 HIS 0.003 0.001 HIS L 193 PHE 0.009 0.001 PHE I 208 TYR 0.020 0.002 TYR F 161 ARG 0.007 0.001 ARG F 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 297 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7504 (mtt180) cc_final: 0.6782 (mpp-170) REVERT: J 417 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7172 (pp) REVERT: K 394 LYS cc_start: 0.9387 (ttmt) cc_final: 0.8958 (ttmm) REVERT: L 112 MET cc_start: 0.7662 (tpt) cc_final: 0.7297 (tpp) REVERT: L 168 ASP cc_start: 0.8862 (t0) cc_final: 0.8606 (t0) REVERT: B 387 MET cc_start: 0.8199 (mtt) cc_final: 0.7949 (mtp) REVERT: B 394 LYS cc_start: 0.9360 (ttmt) cc_final: 0.8999 (ttmm) REVERT: C 112 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7417 (tpp) REVERT: C 136 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8605 (tt) REVERT: C 168 ASP cc_start: 0.8841 (t70) cc_final: 0.8175 (t70) REVERT: C 265 THR cc_start: 0.8863 (OUTLIER) cc_final: 0.8284 (t) REVERT: D 412 ARG cc_start: 0.7724 (mtt180) cc_final: 0.6807 (mpp-170) REVERT: E 388 PHE cc_start: 0.8249 (m-10) cc_final: 0.7912 (m-80) REVERT: E 394 LYS cc_start: 0.9454 (ttmt) cc_final: 0.9027 (ttmm) REVERT: F 168 ASP cc_start: 0.8896 (t70) cc_final: 0.8258 (t70) REVERT: F 189 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.7652 (pmmt) REVERT: F 265 THR cc_start: 0.8883 (p) cc_final: 0.8570 (t) REVERT: G 412 ARG cc_start: 0.7470 (mtt180) cc_final: 0.6862 (mpp-170) REVERT: G 436 MET cc_start: 0.8286 (tmm) cc_final: 0.8025 (tmm) REVERT: H 386 TYR cc_start: 0.8904 (t80) cc_final: 0.8602 (t80) REVERT: H 394 LYS cc_start: 0.9411 (ttmt) cc_final: 0.8890 (ttmm) REVERT: I 112 MET cc_start: 0.7868 (ttm) cc_final: 0.7417 (tpt) REVERT: I 168 ASP cc_start: 0.8994 (t70) cc_final: 0.8696 (t0) REVERT: I 204 SER cc_start: 0.9262 (t) cc_final: 0.8780 (p) REVERT: I 240 ASN cc_start: 0.9027 (t0) cc_final: 0.8805 (t0) REVERT: I 266 GLU cc_start: 0.7830 (pm20) cc_final: 0.7540 (pm20) REVERT: M 412 ARG cc_start: 0.7569 (mtt180) cc_final: 0.6823 (mpp-170) REVERT: M 436 MET cc_start: 0.8494 (tmm) cc_final: 0.8168 (tmm) REVERT: N 394 LYS cc_start: 0.9364 (ttmt) cc_final: 0.9099 (ttmm) REVERT: O 133 TYR cc_start: 0.9049 (m-80) cc_final: 0.8796 (m-80) REVERT: O 204 SER cc_start: 0.9224 (t) cc_final: 0.8671 (p) REVERT: O 240 ASN cc_start: 0.9218 (t0) cc_final: 0.8998 (t0) REVERT: O 265 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8527 (t) REVERT: O 266 GLU cc_start: 0.7812 (pm20) cc_final: 0.7427 (pm20) outliers start: 64 outliers final: 47 residues processed: 340 average time/residue: 0.2204 time to fit residues: 99.5883 Evaluate side-chains 341 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 288 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain K residue 411 LEU Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 164 SER Chi-restraints excluded: chain L residue 171 CYS Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain M residue 427 VAL Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 8.9990 chunk 60 optimal weight: 0.0470 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 43 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 overall best weight: 2.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9125 Z= 0.224 Angle : 0.630 9.706 12365 Z= 0.315 Chirality : 0.045 0.162 1435 Planarity : 0.006 0.058 1555 Dihedral : 6.986 85.386 1292 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 6.03 % Allowed : 24.55 % Favored : 69.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.22), residues: 1165 helix: -1.33 (0.28), residues: 325 sheet: -3.21 (0.39), residues: 120 loop : -2.92 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 196 HIS 0.002 0.001 HIS O 193 PHE 0.007 0.001 PHE O 208 TYR 0.020 0.002 TYR I 133 ARG 0.007 0.000 ARG G 437 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 293 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7429 (mtt180) cc_final: 0.6688 (mpp-170) REVERT: J 417 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7006 (pp) REVERT: K 394 LYS cc_start: 0.9241 (ttmt) cc_final: 0.8916 (ttmm) REVERT: L 168 ASP cc_start: 0.8833 (t0) cc_final: 0.8569 (t0) REVERT: L 204 SER cc_start: 0.9265 (t) cc_final: 0.8751 (p) REVERT: B 387 MET cc_start: 0.8123 (mtt) cc_final: 0.7796 (mtp) REVERT: B 394 LYS cc_start: 0.9327 (ttmt) cc_final: 0.8951 (ttmm) REVERT: C 112 MET cc_start: 0.7643 (OUTLIER) cc_final: 0.7433 (tpp) REVERT: C 136 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8585 (tt) REVERT: C 168 ASP cc_start: 0.8813 (t70) cc_final: 0.8133 (t70) REVERT: C 265 THR cc_start: 0.8795 (OUTLIER) cc_final: 0.8223 (t) REVERT: D 412 ARG cc_start: 0.7726 (mtt180) cc_final: 0.6814 (mpp-170) REVERT: D 436 MET cc_start: 0.8460 (tmm) cc_final: 0.8232 (tmm) REVERT: E 388 PHE cc_start: 0.8179 (m-10) cc_final: 0.7868 (m-80) REVERT: E 394 LYS cc_start: 0.9480 (ttmt) cc_final: 0.9082 (ttmm) REVERT: F 112 MET cc_start: 0.6984 (tpp) cc_final: 0.6754 (tpp) REVERT: F 168 ASP cc_start: 0.8861 (t70) cc_final: 0.8217 (t0) REVERT: F 189 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.7649 (pmmt) REVERT: F 265 THR cc_start: 0.8871 (p) cc_final: 0.8367 (t) REVERT: G 412 ARG cc_start: 0.7376 (mtt180) cc_final: 0.6810 (mpp-170) REVERT: H 394 LYS cc_start: 0.9365 (ttmt) cc_final: 0.8883 (ttmm) REVERT: I 112 MET cc_start: 0.7817 (ttm) cc_final: 0.7405 (tpt) REVERT: I 133 TYR cc_start: 0.8636 (m-80) cc_final: 0.8144 (m-80) REVERT: I 168 ASP cc_start: 0.8957 (t70) cc_final: 0.8650 (t0) REVERT: I 203 TYR cc_start: 0.9123 (t80) cc_final: 0.8921 (t80) REVERT: I 204 SER cc_start: 0.9258 (t) cc_final: 0.8792 (p) REVERT: I 266 GLU cc_start: 0.7698 (pm20) cc_final: 0.7425 (pm20) REVERT: M 412 ARG cc_start: 0.7503 (mtt180) cc_final: 0.6761 (mpp-170) REVERT: M 436 MET cc_start: 0.8443 (tmm) cc_final: 0.8014 (tmm) REVERT: N 394 LYS cc_start: 0.9349 (ttmt) cc_final: 0.9082 (ttmm) REVERT: O 133 TYR cc_start: 0.9045 (m-80) cc_final: 0.8722 (m-10) REVERT: O 186 THR cc_start: 0.9414 (t) cc_final: 0.9205 (m) REVERT: O 265 THR cc_start: 0.8844 (OUTLIER) cc_final: 0.8459 (t) REVERT: O 266 GLU cc_start: 0.7889 (pm20) cc_final: 0.7498 (pm20) outliers start: 57 outliers final: 46 residues processed: 326 average time/residue: 0.2131 time to fit residues: 93.0881 Evaluate side-chains 334 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 282 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 417 LEU Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 171 CYS Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain C residue 112 MET Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 6.9990 chunk 95 optimal weight: 20.0000 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 55 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.4088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9125 Z= 0.208 Angle : 0.630 9.333 12365 Z= 0.314 Chirality : 0.044 0.179 1435 Planarity : 0.006 0.058 1555 Dihedral : 6.936 85.934 1292 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.46 % Allowed : 24.66 % Favored : 68.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.23), residues: 1165 helix: -0.72 (0.30), residues: 295 sheet: -3.11 (0.39), residues: 120 loop : -2.50 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 268 HIS 0.002 0.001 HIS F 146 PHE 0.006 0.001 PHE O 208 TYR 0.018 0.002 TYR I 133 ARG 0.011 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 289 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7399 (mtt180) cc_final: 0.6668 (mpp-170) REVERT: K 394 LYS cc_start: 0.9237 (ttmt) cc_final: 0.8890 (ttmm) REVERT: L 203 TYR cc_start: 0.9098 (t80) cc_final: 0.8542 (t80) REVERT: B 387 MET cc_start: 0.7998 (mtt) cc_final: 0.7662 (mtp) REVERT: B 394 LYS cc_start: 0.9318 (ttmt) cc_final: 0.8946 (ttmm) REVERT: C 136 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8572 (tt) REVERT: C 168 ASP cc_start: 0.8793 (t70) cc_final: 0.8116 (t70) REVERT: C 265 THR cc_start: 0.8779 (p) cc_final: 0.8236 (t) REVERT: D 412 ARG cc_start: 0.7741 (mtt180) cc_final: 0.6837 (mpp-170) REVERT: D 436 MET cc_start: 0.8192 (tmm) cc_final: 0.7733 (tmm) REVERT: E 388 PHE cc_start: 0.8176 (m-10) cc_final: 0.7885 (m-80) REVERT: E 394 LYS cc_start: 0.9452 (ttmt) cc_final: 0.9075 (ttmm) REVERT: E 411 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7075 (tp) REVERT: F 168 ASP cc_start: 0.8833 (t70) cc_final: 0.8337 (t0) REVERT: G 412 ARG cc_start: 0.7448 (mtt180) cc_final: 0.6823 (mpp-170) REVERT: H 394 LYS cc_start: 0.9292 (ttmt) cc_final: 0.8861 (ttmm) REVERT: I 112 MET cc_start: 0.7749 (ttm) cc_final: 0.7317 (tpt) REVERT: I 133 TYR cc_start: 0.8717 (m-80) cc_final: 0.8177 (m-80) REVERT: I 168 ASP cc_start: 0.8941 (t70) cc_final: 0.8629 (t0) REVERT: I 204 SER cc_start: 0.9199 (t) cc_final: 0.8730 (p) REVERT: I 266 GLU cc_start: 0.7708 (pm20) cc_final: 0.7437 (pm20) REVERT: M 412 ARG cc_start: 0.7418 (mtt180) cc_final: 0.6662 (mpp-170) REVERT: M 436 MET cc_start: 0.8417 (tmm) cc_final: 0.8018 (tmm) REVERT: N 394 LYS cc_start: 0.9336 (ttmt) cc_final: 0.9068 (ttmm) REVERT: O 133 TYR cc_start: 0.9043 (m-80) cc_final: 0.8728 (m-10) REVERT: O 175 PRO cc_start: 0.9360 (Cg_exo) cc_final: 0.9024 (Cg_endo) REVERT: O 186 THR cc_start: 0.9410 (t) cc_final: 0.9206 (m) REVERT: O 204 SER cc_start: 0.9236 (t) cc_final: 0.8707 (p) REVERT: O 265 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8523 (t) REVERT: O 266 GLU cc_start: 0.7881 (pm20) cc_final: 0.7500 (pm20) outliers start: 61 outliers final: 48 residues processed: 323 average time/residue: 0.2098 time to fit residues: 90.8193 Evaluate side-chains 338 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 287 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 171 CYS Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 136 LEU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 193 HIS Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain E residue 411 LEU Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0000 chunk 60 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 0.7980 chunk 66 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.4340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9125 Z= 0.165 Angle : 0.598 7.720 12365 Z= 0.297 Chirality : 0.043 0.159 1435 Planarity : 0.006 0.057 1555 Dihedral : 6.942 87.782 1292 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 5.19 % Allowed : 26.77 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.22), residues: 1165 helix: -1.06 (0.28), residues: 335 sheet: -3.08 (0.39), residues: 120 loop : -2.63 (0.20), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 196 HIS 0.003 0.001 HIS F 177 PHE 0.006 0.001 PHE I 208 TYR 0.013 0.001 TYR I 133 ARG 0.007 0.000 ARG D 437 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 292 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7330 (mtt180) cc_final: 0.6632 (mpp-170) REVERT: K 394 LYS cc_start: 0.9195 (ttmt) cc_final: 0.8893 (ttmm) REVERT: B 388 PHE cc_start: 0.8471 (m-10) cc_final: 0.8201 (m-80) REVERT: B 394 LYS cc_start: 0.9292 (ttmt) cc_final: 0.8914 (ttmm) REVERT: C 168 ASP cc_start: 0.8759 (t70) cc_final: 0.8105 (t70) REVERT: C 265 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8278 (t) REVERT: D 436 MET cc_start: 0.8103 (tmm) cc_final: 0.7634 (tmm) REVERT: E 388 PHE cc_start: 0.8287 (m-10) cc_final: 0.8032 (m-80) REVERT: E 394 LYS cc_start: 0.9393 (ttmt) cc_final: 0.9001 (ttmm) REVERT: F 168 ASP cc_start: 0.8858 (t70) cc_final: 0.8331 (t0) REVERT: F 189 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8315 (pttm) REVERT: G 412 ARG cc_start: 0.7427 (mtt180) cc_final: 0.6988 (mpp-170) REVERT: H 394 LYS cc_start: 0.9317 (ttmt) cc_final: 0.8929 (ttmm) REVERT: I 112 MET cc_start: 0.7699 (ttm) cc_final: 0.7259 (tpt) REVERT: I 133 TYR cc_start: 0.8720 (m-80) cc_final: 0.8335 (m-80) REVERT: I 168 ASP cc_start: 0.8885 (t70) cc_final: 0.8612 (t0) REVERT: I 169 LEU cc_start: 0.9564 (mt) cc_final: 0.9295 (mt) REVERT: I 204 SER cc_start: 0.9149 (t) cc_final: 0.8672 (p) REVERT: I 266 GLU cc_start: 0.7673 (pm20) cc_final: 0.7397 (pm20) REVERT: M 412 ARG cc_start: 0.7371 (mtt180) cc_final: 0.6519 (mpp-170) REVERT: M 436 MET cc_start: 0.8368 (tmm) cc_final: 0.7901 (tmm) REVERT: N 388 PHE cc_start: 0.8259 (m-80) cc_final: 0.7970 (m-80) REVERT: N 394 LYS cc_start: 0.9325 (ttmt) cc_final: 0.9046 (ttmm) REVERT: N 411 LEU cc_start: 0.6625 (OUTLIER) cc_final: 0.6391 (tp) REVERT: O 133 TYR cc_start: 0.8994 (m-80) cc_final: 0.8560 (m-80) REVERT: O 175 PRO cc_start: 0.9359 (Cg_exo) cc_final: 0.9010 (Cg_endo) REVERT: O 186 THR cc_start: 0.9381 (t) cc_final: 0.9143 (m) REVERT: O 204 SER cc_start: 0.9164 (t) cc_final: 0.8632 (p) REVERT: O 265 THR cc_start: 0.8861 (OUTLIER) cc_final: 0.8315 (t) REVERT: O 266 GLU cc_start: 0.7839 (pm20) cc_final: 0.7551 (pm20) outliers start: 49 outliers final: 37 residues processed: 318 average time/residue: 0.2103 time to fit residues: 90.3787 Evaluate side-chains 324 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 283 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 174 ILE Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 436 MET Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain H residue 411 LEU Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 96 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 92 optimal weight: 3.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9125 Z= 0.374 Angle : 0.729 10.224 12365 Z= 0.364 Chirality : 0.048 0.159 1435 Planarity : 0.007 0.063 1555 Dihedral : 7.153 87.601 1292 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.56 % Favored : 89.44 % Rotamer: Outliers : 6.67 % Allowed : 24.97 % Favored : 68.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.22), residues: 1165 helix: -1.16 (0.28), residues: 330 sheet: -3.10 (0.41), residues: 120 loop : -2.81 (0.20), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP I 196 HIS 0.005 0.001 HIS I 193 PHE 0.013 0.002 PHE F 208 TYR 0.020 0.002 TYR F 161 ARG 0.014 0.001 ARG G 437 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 303 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7502 (mtt180) cc_final: 0.6750 (mpp-170) REVERT: K 394 LYS cc_start: 0.9219 (ttmt) cc_final: 0.8899 (ttmm) REVERT: L 203 TYR cc_start: 0.9169 (t80) cc_final: 0.8651 (t80) REVERT: B 388 PHE cc_start: 0.8378 (m-10) cc_final: 0.8089 (m-80) REVERT: B 394 LYS cc_start: 0.9335 (ttmt) cc_final: 0.8950 (ttmm) REVERT: C 168 ASP cc_start: 0.8893 (t70) cc_final: 0.8346 (t0) REVERT: C 265 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8180 (t) REVERT: D 412 ARG cc_start: 0.7725 (mtt180) cc_final: 0.6794 (mpp-170) REVERT: E 388 PHE cc_start: 0.8043 (m-10) cc_final: 0.7730 (m-80) REVERT: E 394 LYS cc_start: 0.9355 (ttmt) cc_final: 0.9005 (ttmm) REVERT: F 189 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.7658 (pmmt) REVERT: F 266 GLU cc_start: 0.7912 (pm20) cc_final: 0.7689 (pm20) REVERT: G 412 ARG cc_start: 0.7620 (mtt180) cc_final: 0.6837 (mpp-170) REVERT: G 436 MET cc_start: 0.8368 (tmm) cc_final: 0.7931 (tmm) REVERT: H 386 TYR cc_start: 0.8908 (t80) cc_final: 0.8447 (t80) REVERT: H 394 LYS cc_start: 0.9395 (ttmt) cc_final: 0.8942 (ttmm) REVERT: I 133 TYR cc_start: 0.8932 (m-80) cc_final: 0.8343 (m-80) REVERT: I 168 ASP cc_start: 0.8963 (t70) cc_final: 0.8703 (t0) REVERT: I 266 GLU cc_start: 0.7824 (pm20) cc_final: 0.7390 (pm20) REVERT: M 412 ARG cc_start: 0.7609 (mtt180) cc_final: 0.6886 (mpp-170) REVERT: M 436 MET cc_start: 0.8645 (tmm) cc_final: 0.8188 (tmm) REVERT: N 394 LYS cc_start: 0.9345 (ttmt) cc_final: 0.9080 (ttmm) REVERT: N 411 LEU cc_start: 0.7285 (OUTLIER) cc_final: 0.7083 (tp) REVERT: O 133 TYR cc_start: 0.9215 (m-80) cc_final: 0.8981 (m-10) REVERT: O 266 GLU cc_start: 0.7908 (pm20) cc_final: 0.7636 (pm20) outliers start: 63 outliers final: 49 residues processed: 337 average time/residue: 0.2069 time to fit residues: 94.2058 Evaluate side-chains 337 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 285 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain J residue 427 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain A residue 427 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain D residue 427 VAL Chi-restraints excluded: chain D residue 437 ARG Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 258 THR Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 427 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain I residue 165 SER Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain N residue 411 LEU Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 151 ILE Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 164 SER Chi-restraints excluded: chain O residue 258 THR Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 101 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 64 optimal weight: 8.9990 chunk 104 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9125 Z= 0.207 Angle : 0.647 8.576 12365 Z= 0.322 Chirality : 0.045 0.169 1435 Planarity : 0.006 0.058 1555 Dihedral : 7.006 86.946 1292 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 5.19 % Allowed : 28.36 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.23), residues: 1165 helix: -0.34 (0.31), residues: 295 sheet: -3.07 (0.40), residues: 120 loop : -2.33 (0.21), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP O 196 HIS 0.014 0.001 HIS F 146 PHE 0.007 0.001 PHE I 208 TYR 0.016 0.001 TYR I 203 ARG 0.010 0.000 ARG G 437 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 281 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7409 (mtt180) cc_final: 0.6671 (mpp-170) REVERT: K 394 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8856 (ttmm) REVERT: L 203 TYR cc_start: 0.9159 (t80) cc_final: 0.8699 (t80) REVERT: B 388 PHE cc_start: 0.8433 (m-10) cc_final: 0.8184 (m-80) REVERT: B 394 LYS cc_start: 0.9285 (ttmt) cc_final: 0.8907 (ttmm) REVERT: C 168 ASP cc_start: 0.8799 (t70) cc_final: 0.8111 (t0) REVERT: C 265 THR cc_start: 0.8806 (OUTLIER) cc_final: 0.8251 (t) REVERT: D 436 MET cc_start: 0.8172 (tmm) cc_final: 0.7643 (tmm) REVERT: E 388 PHE cc_start: 0.8246 (m-10) cc_final: 0.7982 (m-80) REVERT: E 394 LYS cc_start: 0.9295 (ttmt) cc_final: 0.8951 (ttmm) REVERT: F 266 GLU cc_start: 0.7766 (pm20) cc_final: 0.7533 (pm20) REVERT: G 412 ARG cc_start: 0.7574 (mtt180) cc_final: 0.6813 (mpp-170) REVERT: H 394 LYS cc_start: 0.9351 (ttmt) cc_final: 0.8882 (ttmm) REVERT: I 133 TYR cc_start: 0.8825 (m-80) cc_final: 0.8283 (m-80) REVERT: I 168 ASP cc_start: 0.8940 (t70) cc_final: 0.8679 (t0) REVERT: I 169 LEU cc_start: 0.9563 (mt) cc_final: 0.9306 (mt) REVERT: I 204 SER cc_start: 0.9218 (t) cc_final: 0.8759 (p) REVERT: I 266 GLU cc_start: 0.7751 (pm20) cc_final: 0.7344 (pm20) REVERT: M 412 ARG cc_start: 0.7508 (mtt180) cc_final: 0.6764 (mpp-170) REVERT: M 436 MET cc_start: 0.8450 (tmm) cc_final: 0.7973 (tmm) REVERT: N 394 LYS cc_start: 0.9288 (ttmt) cc_final: 0.9028 (ttmm) REVERT: O 133 TYR cc_start: 0.9185 (m-80) cc_final: 0.8955 (m-10) REVERT: O 266 GLU cc_start: 0.7836 (pm20) cc_final: 0.7576 (pm20) outliers start: 49 outliers final: 41 residues processed: 304 average time/residue: 0.2043 time to fit residues: 83.8874 Evaluate side-chains 319 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 277 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 165 SER Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 186 THR Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 67 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 92 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.4437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9125 Z= 0.199 Angle : 0.640 8.260 12365 Z= 0.316 Chirality : 0.045 0.153 1435 Planarity : 0.006 0.058 1555 Dihedral : 6.928 86.628 1292 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 4.44 % Allowed : 29.63 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.23), residues: 1165 helix: -0.59 (0.30), residues: 325 sheet: -3.02 (0.40), residues: 120 loop : -2.54 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 268 HIS 0.015 0.001 HIS F 146 PHE 0.006 0.001 PHE O 208 TYR 0.016 0.001 TYR I 203 ARG 0.011 0.000 ARG G 437 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 281 time to evaluate : 1.020 Fit side-chains revert: symmetry clash REVERT: J 412 ARG cc_start: 0.7377 (mtt180) cc_final: 0.6656 (mpp-170) REVERT: K 394 LYS cc_start: 0.9166 (ttmt) cc_final: 0.8847 (ttmm) REVERT: L 112 MET cc_start: 0.7808 (tpt) cc_final: 0.7391 (tpp) REVERT: L 203 TYR cc_start: 0.9164 (t80) cc_final: 0.8726 (t80) REVERT: B 388 PHE cc_start: 0.8418 (m-10) cc_final: 0.8169 (m-80) REVERT: B 394 LYS cc_start: 0.9272 (ttmt) cc_final: 0.8882 (ttmm) REVERT: C 168 ASP cc_start: 0.8798 (t70) cc_final: 0.8132 (t0) REVERT: C 265 THR cc_start: 0.8765 (OUTLIER) cc_final: 0.8240 (t) REVERT: D 436 MET cc_start: 0.8287 (tmm) cc_final: 0.7767 (tmm) REVERT: E 388 PHE cc_start: 0.8242 (m-10) cc_final: 0.7984 (m-80) REVERT: E 394 LYS cc_start: 0.9281 (ttmt) cc_final: 0.8939 (ttmm) REVERT: G 412 ARG cc_start: 0.7556 (mtt180) cc_final: 0.6942 (mpp-170) REVERT: H 394 LYS cc_start: 0.9265 (ttmt) cc_final: 0.8863 (ttmm) REVERT: I 133 TYR cc_start: 0.8814 (m-80) cc_final: 0.8255 (m-80) REVERT: I 168 ASP cc_start: 0.8921 (t70) cc_final: 0.8655 (t0) REVERT: I 169 LEU cc_start: 0.9556 (mt) cc_final: 0.9295 (mt) REVERT: I 204 SER cc_start: 0.9151 (t) cc_final: 0.8658 (p) REVERT: I 266 GLU cc_start: 0.7769 (pm20) cc_final: 0.7386 (pm20) REVERT: M 412 ARG cc_start: 0.7487 (mtt180) cc_final: 0.6754 (mpp-170) REVERT: M 436 MET cc_start: 0.8432 (tmm) cc_final: 0.7956 (tmm) REVERT: N 394 LYS cc_start: 0.9277 (ttmt) cc_final: 0.9011 (ttmm) REVERT: O 133 TYR cc_start: 0.9043 (m-80) cc_final: 0.8571 (m-80) REVERT: O 266 GLU cc_start: 0.7817 (pm20) cc_final: 0.7546 (pm20) outliers start: 42 outliers final: 39 residues processed: 303 average time/residue: 0.2025 time to fit residues: 82.9989 Evaluate side-chains 316 residues out of total 945 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 276 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 425 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 114 MET Chi-restraints excluded: chain L residue 119 ASP Chi-restraints excluded: chain L residue 124 VAL Chi-restraints excluded: chain L residue 136 LEU Chi-restraints excluded: chain L residue 158 LYS Chi-restraints excluded: chain L residue 186 THR Chi-restraints excluded: chain A residue 425 VAL Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain C residue 119 ASP Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 158 LYS Chi-restraints excluded: chain C residue 165 SER Chi-restraints excluded: chain C residue 174 ILE Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 425 VAL Chi-restraints excluded: chain E residue 397 THR Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 124 VAL Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain F residue 184 LYS Chi-restraints excluded: chain F residue 189 LYS Chi-restraints excluded: chain F residue 193 HIS Chi-restraints excluded: chain G residue 425 VAL Chi-restraints excluded: chain G residue 432 THR Chi-restraints excluded: chain H residue 397 THR Chi-restraints excluded: chain I residue 116 ILE Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 131 THR Chi-restraints excluded: chain I residue 158 LYS Chi-restraints excluded: chain M residue 425 VAL Chi-restraints excluded: chain N residue 397 THR Chi-restraints excluded: chain O residue 119 ASP Chi-restraints excluded: chain O residue 124 VAL Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 158 LYS Chi-restraints excluded: chain O residue 265 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.108362 restraints weight = 14789.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111390 restraints weight = 7570.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113495 restraints weight = 4711.435| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9125 Z= 0.250 Angle : 0.678 8.419 12365 Z= 0.336 Chirality : 0.046 0.164 1435 Planarity : 0.006 0.058 1555 Dihedral : 7.012 87.971 1292 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.97 % Allowed : 29.21 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.23), residues: 1165 helix: -0.68 (0.30), residues: 330 sheet: -3.00 (0.41), residues: 120 loop : -2.53 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP O 196 HIS 0.014 0.001 HIS F 146 PHE 0.008 0.001 PHE F 208 TYR 0.017 0.002 TYR I 203 ARG 0.011 0.000 ARG G 437 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2254.64 seconds wall clock time: 347 minutes 46.62 seconds (20866.62 seconds total)