Starting phenix.real_space_refine on Fri Feb 16 11:50:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/02_2024/6nil_9380.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/02_2024/6nil_9380.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/02_2024/6nil_9380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/02_2024/6nil_9380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/02_2024/6nil_9380.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/02_2024/6nil_9380.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 80 5.16 5 C 9696 2.51 5 N 2708 2.21 5 O 2732 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 208": "NH1" <-> "NH2" Residue "A ARG 235": "NH1" <-> "NH2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 23": "NH1" <-> "NH2" Residue "C ARG 41": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "D ARG 208": "NH1" <-> "NH2" Residue "D ARG 235": "NH1" <-> "NH2" Residue "D ARG 252": "NH1" <-> "NH2" Residue "D GLU 289": "OE1" <-> "OE2" Residue "E ARG 90": "NH1" <-> "NH2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F ARG 41": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "G ARG 208": "NH1" <-> "NH2" Residue "G ARG 235": "NH1" <-> "NH2" Residue "G ARG 252": "NH1" <-> "NH2" Residue "G GLU 289": "OE1" <-> "OE2" Residue "H ARG 90": "NH1" <-> "NH2" Residue "I ARG 15": "NH1" <-> "NH2" Residue "I ARG 23": "NH1" <-> "NH2" Residue "I ARG 41": "NH1" <-> "NH2" Residue "I ARG 90": "NH1" <-> "NH2" Residue "J ARG 208": "NH1" <-> "NH2" Residue "J ARG 235": "NH1" <-> "NH2" Residue "J ARG 252": "NH1" <-> "NH2" Residue "J GLU 289": "OE1" <-> "OE2" Residue "K ARG 90": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "L ARG 23": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 90": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15220 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1485 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 1 Chain: "B" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1167 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "C" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1152 Classifications: {'peptide': 133} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "D" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1485 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 1 Chain: "E" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1167 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "F" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1152 Classifications: {'peptide': 133} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "G" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1485 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 1 Chain: "H" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1167 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "I" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1152 Classifications: {'peptide': 133} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "J" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1485 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 8, 'TRANS': 168} Chain breaks: 1 Chain: "K" Number of atoms: 1167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1167 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 4, 'TRANS': 135} Chain breaks: 1 Chain: "L" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1152 Classifications: {'peptide': 133} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 5, 'TRANS': 125} Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 723 SG CYS A 280 39.786 37.844 58.515 1.00162.43 S ATOM 745 SG CYS A 283 39.236 37.059 55.226 1.00169.71 S ATOM 4527 SG CYS D 280 82.014 69.256 58.515 1.00162.43 S ATOM 4549 SG CYS D 283 82.564 70.041 55.226 1.00169.71 S ATOM 8331 SG CYS G 280 82.014 37.844 29.685 1.00162.43 S ATOM 8353 SG CYS G 283 82.564 37.059 32.974 1.00169.71 S ATOM 12135 SG CYS J 280 39.786 69.256 29.685 1.00162.43 S ATOM 12157 SG CYS J 283 39.236 70.041 32.974 1.00169.71 S Time building chain proxies: 7.38, per 1000 atoms: 0.48 Number of scatterers: 15220 At special positions: 0 Unit cell: (122.85, 108.15, 89.25, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 80 16.00 O 2732 8.00 N 2708 7.00 C 9696 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: 5.03 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 280 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 283 " pdb="ZN ZN A 501 " - pdb=" ND1 HIS A 249 " pdb=" ZN D 501 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 280 " pdb="ZN ZN D 501 " - pdb=" SG CYS D 283 " pdb="ZN ZN D 501 " - pdb=" ND1 HIS D 249 " pdb=" ZN G 501 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 280 " pdb="ZN ZN G 501 " - pdb=" SG CYS G 283 " pdb="ZN ZN G 501 " - pdb=" ND1 HIS G 249 " pdb=" ZN J 501 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 280 " pdb="ZN ZN J 501 " - pdb=" SG CYS J 283 " pdb="ZN ZN J 501 " - pdb=" ND1 HIS J 249 " 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 20 sheets defined 31.3% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 196 through 204 removed outlier: 3.744A pdb=" N PHE A 202 " --> pdb=" O HIS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 259 removed outlier: 4.185A pdb=" N LEU A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 294 removed outlier: 5.614A pdb=" N GLU A 289 " --> pdb=" O GLY A 285 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE A 290 " --> pdb=" O GLU A 286 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 291 " --> pdb=" O VAL A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 321 removed outlier: 3.600A pdb=" N ALA A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU A 316 " --> pdb=" O THR A 312 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 317 " --> pdb=" O ASP A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 325 removed outlier: 3.893A pdb=" N GLY A 325 " --> pdb=" O SER A 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 322 through 325' Processing helix chain 'A' and resid 332 through 344 removed outlier: 3.740A pdb=" N LYS A 337 " --> pdb=" O TYR A 333 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR A 338 " --> pdb=" O LYS A 334 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 370 removed outlier: 3.920A pdb=" N LEU A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP A 363 " --> pdb=" O TYR A 359 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 367 " --> pdb=" O ASP A 363 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 15 removed outlier: 3.503A pdb=" N PHE B 12 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU B 13 " --> pdb=" O ARG B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 22 Processing helix chain 'B' and resid 39 through 50 removed outlier: 4.537A pdb=" N ARG B 49 " --> pdb=" O GLN B 45 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP B 50 " --> pdb=" O ASN B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 134 removed outlier: 3.837A pdb=" N GLN B 133 " --> pdb=" O GLU B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 144 removed outlier: 3.556A pdb=" N PHE B 143 " --> pdb=" O GLN B 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 25 removed outlier: 4.651A pdb=" N ARG C 23 " --> pdb=" O ASN C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 removed outlier: 3.597A pdb=" N ASP C 104 " --> pdb=" O PRO C 100 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 170 removed outlier: 3.513A pdb=" N LEU C 169 " --> pdb=" O SER C 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 196 through 204 removed outlier: 3.744A pdb=" N PHE D 202 " --> pdb=" O HIS D 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 259 removed outlier: 4.185A pdb=" N LEU D 255 " --> pdb=" O GLU D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 294 removed outlier: 5.614A pdb=" N GLU D 289 " --> pdb=" O GLY D 285 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE D 290 " --> pdb=" O GLU D 286 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 291 " --> pdb=" O VAL D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 321 removed outlier: 3.600A pdb=" N ALA D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU D 316 " --> pdb=" O THR D 312 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY D 317 " --> pdb=" O ASP D 313 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 325 removed outlier: 3.893A pdb=" N GLY D 325 " --> pdb=" O SER D 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 322 through 325' Processing helix chain 'D' and resid 332 through 344 removed outlier: 3.740A pdb=" N LYS D 337 " --> pdb=" O TYR D 333 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL D 344 " --> pdb=" O TRP D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 370 removed outlier: 3.920A pdb=" N LEU D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP D 363 " --> pdb=" O TYR D 359 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 364 " --> pdb=" O ASN D 360 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS D 367 " --> pdb=" O ASP D 363 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU D 368 " --> pdb=" O LEU D 364 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 15 removed outlier: 3.503A pdb=" N PHE E 12 " --> pdb=" O GLN E 8 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU E 13 " --> pdb=" O ARG E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 22 Processing helix chain 'E' and resid 39 through 50 removed outlier: 4.537A pdb=" N ARG E 49 " --> pdb=" O GLN E 45 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 134 removed outlier: 3.837A pdb=" N GLN E 133 " --> pdb=" O GLU E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 144 removed outlier: 3.556A pdb=" N PHE E 143 " --> pdb=" O GLN E 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 25 removed outlier: 4.651A pdb=" N ARG F 23 " --> pdb=" O ASN F 19 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 108 removed outlier: 3.597A pdb=" N ASP F 104 " --> pdb=" O PRO F 100 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 170 removed outlier: 3.513A pdb=" N LEU F 169 " --> pdb=" O SER F 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 204 removed outlier: 3.744A pdb=" N PHE G 202 " --> pdb=" O HIS G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 259 removed outlier: 4.185A pdb=" N LEU G 255 " --> pdb=" O GLU G 251 " (cutoff:3.500A) Processing helix chain 'G' and resid 283 through 294 removed outlier: 5.614A pdb=" N GLU G 289 " --> pdb=" O GLY G 285 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE G 290 " --> pdb=" O GLU G 286 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU G 291 " --> pdb=" O VAL G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 311 through 321 removed outlier: 3.600A pdb=" N ALA G 315 " --> pdb=" O ASP G 311 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU G 316 " --> pdb=" O THR G 312 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY G 317 " --> pdb=" O ASP G 313 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 325 removed outlier: 3.893A pdb=" N GLY G 325 " --> pdb=" O SER G 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 322 through 325' Processing helix chain 'G' and resid 332 through 344 removed outlier: 3.740A pdb=" N LYS G 337 " --> pdb=" O TYR G 333 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR G 338 " --> pdb=" O LYS G 334 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL G 344 " --> pdb=" O TRP G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 356 through 370 removed outlier: 3.920A pdb=" N LEU G 362 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP G 363 " --> pdb=" O TYR G 359 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU G 364 " --> pdb=" O ASN G 360 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS G 367 " --> pdb=" O ASP G 363 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU G 368 " --> pdb=" O LEU G 364 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 removed outlier: 3.503A pdb=" N PHE H 12 " --> pdb=" O GLN H 8 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU H 13 " --> pdb=" O ARG H 9 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 22 Processing helix chain 'H' and resid 39 through 50 removed outlier: 4.537A pdb=" N ARG H 49 " --> pdb=" O GLN H 45 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP H 50 " --> pdb=" O ASN H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 134 removed outlier: 3.837A pdb=" N GLN H 133 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 144 removed outlier: 3.556A pdb=" N PHE H 143 " --> pdb=" O GLN H 140 " (cutoff:3.500A) Processing helix chain 'I' and resid 17 through 25 removed outlier: 4.651A pdb=" N ARG I 23 " --> pdb=" O ASN I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 108 removed outlier: 3.597A pdb=" N ASP I 104 " --> pdb=" O PRO I 100 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN I 105 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 165 through 170 removed outlier: 3.513A pdb=" N LEU I 169 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 196 through 204 removed outlier: 3.744A pdb=" N PHE J 202 " --> pdb=" O HIS J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 249 through 259 removed outlier: 4.185A pdb=" N LEU J 255 " --> pdb=" O GLU J 251 " (cutoff:3.500A) Processing helix chain 'J' and resid 283 through 294 removed outlier: 5.614A pdb=" N GLU J 289 " --> pdb=" O GLY J 285 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N PHE J 290 " --> pdb=" O GLU J 286 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU J 291 " --> pdb=" O VAL J 287 " (cutoff:3.500A) Processing helix chain 'J' and resid 311 through 321 removed outlier: 3.600A pdb=" N ALA J 315 " --> pdb=" O ASP J 311 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU J 316 " --> pdb=" O THR J 312 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY J 317 " --> pdb=" O ASP J 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 322 through 325 removed outlier: 3.893A pdb=" N GLY J 325 " --> pdb=" O SER J 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 322 through 325' Processing helix chain 'J' and resid 332 through 344 removed outlier: 3.740A pdb=" N LYS J 337 " --> pdb=" O TYR J 333 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N TYR J 338 " --> pdb=" O LYS J 334 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL J 344 " --> pdb=" O TRP J 340 " (cutoff:3.500A) Processing helix chain 'J' and resid 356 through 370 removed outlier: 3.920A pdb=" N LEU J 362 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N ASP J 363 " --> pdb=" O TYR J 359 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU J 364 " --> pdb=" O ASN J 360 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS J 367 " --> pdb=" O ASP J 363 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU J 368 " --> pdb=" O LEU J 364 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 removed outlier: 3.503A pdb=" N PHE K 12 " --> pdb=" O GLN K 8 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU K 13 " --> pdb=" O ARG K 9 " (cutoff:3.500A) Processing helix chain 'K' and resid 15 through 22 Processing helix chain 'K' and resid 39 through 50 removed outlier: 4.537A pdb=" N ARG K 49 " --> pdb=" O GLN K 45 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ASP K 50 " --> pdb=" O ASN K 46 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 134 removed outlier: 3.837A pdb=" N GLN K 133 " --> pdb=" O GLU K 130 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 144 removed outlier: 3.556A pdb=" N PHE K 143 " --> pdb=" O GLN K 140 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 25 removed outlier: 4.651A pdb=" N ARG L 23 " --> pdb=" O ASN L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 108 removed outlier: 3.597A pdb=" N ASP L 104 " --> pdb=" O PRO L 100 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N GLN L 105 " --> pdb=" O ASP L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 170 removed outlier: 3.513A pdb=" N LEU L 169 " --> pdb=" O SER L 165 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 238 removed outlier: 3.696A pdb=" N GLY A 236 " --> pdb=" O PHE A 220 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 303 removed outlier: 6.380A pdb=" N GLU A 329 " --> pdb=" O THR A 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 26 through 27 removed outlier: 3.655A pdb=" N LYS B 111 " --> pdb=" O CYS B 124 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE B 114 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL B 95 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N LYS B 94 " --> pdb=" O GLU B 89 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLU B 89 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 96 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP B 87 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS B 98 " --> pdb=" O TYR B 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 56 through 58 removed outlier: 3.989A pdb=" N GLN B 67 " --> pdb=" O MET C 8 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET C 8 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 13.643A pdb=" N VAL C 7 " --> pdb=" O TRP C 89 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N TRP C 89 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 9 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE C 87 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN C 83 " --> pdb=" O VAL C 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 86 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR C 67 " --> pdb=" O SER C 86 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 63 " --> pdb=" O ARG C 90 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA C 62 " --> pdb=" O LEU C 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 56 through 58 removed outlier: 3.989A pdb=" N GLN B 67 " --> pdb=" O MET C 8 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET C 8 " --> pdb=" O GLN B 67 " (cutoff:3.500A) removed outlier: 13.643A pdb=" N VAL C 7 " --> pdb=" O TRP C 89 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N TRP C 89 " --> pdb=" O VAL C 7 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 9 " --> pdb=" O ILE C 87 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE C 87 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN C 83 " --> pdb=" O VAL C 13 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 234 through 238 removed outlier: 3.696A pdb=" N GLY D 236 " --> pdb=" O PHE D 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 302 through 303 removed outlier: 6.380A pdb=" N GLU D 329 " --> pdb=" O THR D 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 26 through 27 removed outlier: 3.655A pdb=" N LYS E 111 " --> pdb=" O CYS E 124 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE E 114 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL E 95 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N LYS E 94 " --> pdb=" O GLU E 89 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLU E 89 " --> pdb=" O LYS E 94 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR E 96 " --> pdb=" O ASP E 87 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP E 87 " --> pdb=" O TYR E 96 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 98 " --> pdb=" O TYR E 85 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.989A pdb=" N GLN E 67 " --> pdb=" O MET F 8 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET F 8 " --> pdb=" O GLN E 67 " (cutoff:3.500A) removed outlier: 13.643A pdb=" N VAL F 7 " --> pdb=" O TRP F 89 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N TRP F 89 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 9 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE F 87 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN F 83 " --> pdb=" O VAL F 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER F 86 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR F 67 " --> pdb=" O SER F 86 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS F 63 " --> pdb=" O ARG F 90 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA F 62 " --> pdb=" O LEU F 59 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 56 through 58 removed outlier: 3.989A pdb=" N GLN E 67 " --> pdb=" O MET F 8 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET F 8 " --> pdb=" O GLN E 67 " (cutoff:3.500A) removed outlier: 13.643A pdb=" N VAL F 7 " --> pdb=" O TRP F 89 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N TRP F 89 " --> pdb=" O VAL F 7 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 9 " --> pdb=" O ILE F 87 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE F 87 " --> pdb=" O ILE F 9 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN F 83 " --> pdb=" O VAL F 13 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 234 through 238 removed outlier: 3.696A pdb=" N GLY G 236 " --> pdb=" O PHE G 220 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 302 through 303 removed outlier: 6.380A pdb=" N GLU G 329 " --> pdb=" O THR G 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'H' and resid 26 through 27 removed outlier: 3.655A pdb=" N LYS H 111 " --> pdb=" O CYS H 124 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE H 114 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL H 95 " --> pdb=" O ILE H 114 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N LYS H 94 " --> pdb=" O GLU H 89 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLU H 89 " --> pdb=" O LYS H 94 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR H 96 " --> pdb=" O ASP H 87 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP H 87 " --> pdb=" O TYR H 96 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS H 98 " --> pdb=" O TYR H 85 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 56 through 58 removed outlier: 3.989A pdb=" N GLN H 67 " --> pdb=" O MET I 8 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET I 8 " --> pdb=" O GLN H 67 " (cutoff:3.500A) removed outlier: 13.643A pdb=" N VAL I 7 " --> pdb=" O TRP I 89 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N TRP I 89 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE I 9 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE I 87 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER I 86 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR I 67 " --> pdb=" O SER I 86 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS I 63 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA I 62 " --> pdb=" O LEU I 59 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 56 through 58 removed outlier: 3.989A pdb=" N GLN H 67 " --> pdb=" O MET I 8 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET I 8 " --> pdb=" O GLN H 67 " (cutoff:3.500A) removed outlier: 13.643A pdb=" N VAL I 7 " --> pdb=" O TRP I 89 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N TRP I 89 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE I 9 " --> pdb=" O ILE I 87 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE I 87 " --> pdb=" O ILE I 9 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN I 83 " --> pdb=" O VAL I 13 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 234 through 238 removed outlier: 3.696A pdb=" N GLY J 236 " --> pdb=" O PHE J 220 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 302 through 303 removed outlier: 6.380A pdb=" N GLU J 329 " --> pdb=" O THR J 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'K' and resid 26 through 27 removed outlier: 3.655A pdb=" N LYS K 111 " --> pdb=" O CYS K 124 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE K 114 " --> pdb=" O VAL K 95 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL K 95 " --> pdb=" O ILE K 114 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N LYS K 94 " --> pdb=" O GLU K 89 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLU K 89 " --> pdb=" O LYS K 94 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR K 96 " --> pdb=" O ASP K 87 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASP K 87 " --> pdb=" O TYR K 96 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS K 98 " --> pdb=" O TYR K 85 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 56 through 58 removed outlier: 3.989A pdb=" N GLN K 67 " --> pdb=" O MET L 8 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET L 8 " --> pdb=" O GLN K 67 " (cutoff:3.500A) removed outlier: 13.643A pdb=" N VAL L 7 " --> pdb=" O TRP L 89 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N TRP L 89 " --> pdb=" O VAL L 7 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE L 9 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE L 87 " --> pdb=" O ILE L 9 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN L 83 " --> pdb=" O VAL L 13 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER L 86 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N THR L 67 " --> pdb=" O SER L 86 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS L 63 " --> pdb=" O ARG L 90 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA L 62 " --> pdb=" O LEU L 59 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 56 through 58 removed outlier: 3.989A pdb=" N GLN K 67 " --> pdb=" O MET L 8 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N MET L 8 " --> pdb=" O GLN K 67 " (cutoff:3.500A) removed outlier: 13.643A pdb=" N VAL L 7 " --> pdb=" O TRP L 89 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N TRP L 89 " --> pdb=" O VAL L 7 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE L 9 " --> pdb=" O ILE L 87 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N ILE L 87 " --> pdb=" O ILE L 9 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLN L 83 " --> pdb=" O VAL L 13 " (cutoff:3.500A) 440 hydrogen bonds defined for protein. 1224 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: 3.75 Time building geometry restraints manager: 5.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 4972 1.35 - 1.47: 4176 1.47 - 1.60: 6380 1.60 - 1.72: 0 1.72 - 1.85: 120 Bond restraints: 15648 Sorted by residual: bond pdb=" CA VAL H 5 " pdb=" C VAL H 5 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.05e-02 9.07e+03 1.03e+01 bond pdb=" CA VAL K 5 " pdb=" C VAL K 5 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.05e-02 9.07e+03 1.03e+01 bond pdb=" CA VAL E 5 " pdb=" C VAL E 5 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.05e-02 9.07e+03 1.03e+01 bond pdb=" CA VAL B 5 " pdb=" C VAL B 5 " ideal model delta sigma weight residual 1.524 1.558 -0.034 1.05e-02 9.07e+03 1.03e+01 bond pdb=" C ARG H 23 " pdb=" N GLU H 24 " ideal model delta sigma weight residual 1.332 1.373 -0.040 1.40e-02 5.10e+03 8.34e+00 ... (remaining 15643 not shown) Histogram of bond angle deviations from ideal: 100.20 - 107.13: 532 107.13 - 114.06: 8376 114.06 - 120.99: 7376 120.99 - 127.92: 4596 127.92 - 134.85: 252 Bond angle restraints: 21132 Sorted by residual: angle pdb=" N GLN L 83 " pdb=" CA GLN L 83 " pdb=" CB GLN L 83 " ideal model delta sigma weight residual 110.77 100.92 9.85 1.57e+00 4.06e-01 3.94e+01 angle pdb=" N GLN C 83 " pdb=" CA GLN C 83 " pdb=" CB GLN C 83 " ideal model delta sigma weight residual 110.77 100.92 9.85 1.57e+00 4.06e-01 3.94e+01 angle pdb=" N GLN I 83 " pdb=" CA GLN I 83 " pdb=" CB GLN I 83 " ideal model delta sigma weight residual 110.77 100.92 9.85 1.57e+00 4.06e-01 3.94e+01 angle pdb=" N GLN F 83 " pdb=" CA GLN F 83 " pdb=" CB GLN F 83 " ideal model delta sigma weight residual 110.77 100.92 9.85 1.57e+00 4.06e-01 3.94e+01 angle pdb=" C VAL H 5 " pdb=" N PRO H 6 " pdb=" CA PRO H 6 " ideal model delta sigma weight residual 119.64 114.85 4.79 1.01e+00 9.80e-01 2.25e+01 ... (remaining 21127 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 8444 17.97 - 35.94: 648 35.94 - 53.91: 124 53.91 - 71.88: 8 71.88 - 89.85: 8 Dihedral angle restraints: 9232 sinusoidal: 3940 harmonic: 5292 Sorted by residual: dihedral pdb=" CA GLU K 144 " pdb=" C GLU K 144 " pdb=" N GLU K 145 " pdb=" CA GLU K 145 " ideal model delta harmonic sigma weight residual 180.00 145.25 34.75 0 5.00e+00 4.00e-02 4.83e+01 dihedral pdb=" CA GLU E 144 " pdb=" C GLU E 144 " pdb=" N GLU E 145 " pdb=" CA GLU E 145 " ideal model delta harmonic sigma weight residual 180.00 145.25 34.75 0 5.00e+00 4.00e-02 4.83e+01 dihedral pdb=" CA GLU H 144 " pdb=" C GLU H 144 " pdb=" N GLU H 145 " pdb=" CA GLU H 145 " ideal model delta harmonic sigma weight residual 180.00 145.25 34.75 0 5.00e+00 4.00e-02 4.83e+01 ... (remaining 9229 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1648 0.089 - 0.178: 396 0.178 - 0.267: 44 0.267 - 0.356: 12 0.356 - 0.444: 4 Chirality restraints: 2104 Sorted by residual: chirality pdb=" CA ASP F 78 " pdb=" N ASP F 78 " pdb=" C ASP F 78 " pdb=" CB ASP F 78 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA ASP C 78 " pdb=" N ASP C 78 " pdb=" C ASP C 78 " pdb=" CB ASP C 78 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 chirality pdb=" CA ASP I 78 " pdb=" N ASP I 78 " pdb=" C ASP I 78 " pdb=" CB ASP I 78 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.94e+00 ... (remaining 2101 not shown) Planarity restraints: 2728 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 33 " -0.544 9.50e-02 1.11e+02 2.44e-01 3.64e+01 pdb=" NE ARG C 33 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG C 33 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 33 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 33 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 33 " -0.544 9.50e-02 1.11e+02 2.44e-01 3.64e+01 pdb=" NE ARG F 33 " 0.032 2.00e-02 2.50e+03 pdb=" CZ ARG F 33 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG F 33 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG F 33 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 33 " 0.544 9.50e-02 1.11e+02 2.44e-01 3.64e+01 pdb=" NE ARG I 33 " -0.032 2.00e-02 2.50e+03 pdb=" CZ ARG I 33 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG I 33 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG I 33 " 0.018 2.00e-02 2.50e+03 ... (remaining 2725 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 5748 2.90 - 3.40: 13978 3.40 - 3.90: 24444 3.90 - 4.40: 27752 4.40 - 4.90: 46410 Nonbonded interactions: 118332 Sorted by model distance: nonbonded pdb=" O TRP D 277 " pdb=" OG1 THR D 303 " model vdw 2.396 2.440 nonbonded pdb=" O TRP A 277 " pdb=" OG1 THR A 303 " model vdw 2.396 2.440 nonbonded pdb=" O TRP G 277 " pdb=" OG1 THR G 303 " model vdw 2.396 2.440 nonbonded pdb=" O TRP J 277 " pdb=" OG1 THR J 303 " model vdw 2.396 2.440 nonbonded pdb=" O ILE C 107 " pdb=" N TYR C 111 " model vdw 2.459 2.520 ... (remaining 118327 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' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'I' selection = chain 'L' } 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: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.150 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 38.960 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 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 : 0.005 0.042 15648 Z= 0.348 Angle : 0.957 9.851 21132 Z= 0.580 Chirality : 0.079 0.444 2104 Planarity : 0.016 0.244 2728 Dihedral : 13.204 89.850 5792 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.59 % Favored : 90.41 % Rotamer: Outliers : 0.99 % Allowed : 8.89 % Favored : 90.12 % Cbeta Deviations : 0.93 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -4.92 (0.16), residues: 1752 helix: -4.16 (0.12), residues: 516 sheet: -3.04 (0.24), residues: 380 loop : -2.68 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP L 174 HIS 0.006 0.001 HIS A 249 PHE 0.009 0.001 PHE A 200 TYR 0.014 0.002 TYR L 44 ARG 0.005 0.000 ARG D 293 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 636 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 620 time to evaluate : 1.531 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.9332 (tp30) cc_final: 0.9097 (tp30) REVERT: A 207 LEU cc_start: 0.8440 (mm) cc_final: 0.8210 (pt) REVERT: A 248 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7803 (mtp180) REVERT: A 252 ARG cc_start: 0.9447 (ttp80) cc_final: 0.9230 (ttp80) REVERT: A 282 GLU cc_start: 0.8903 (tp30) cc_final: 0.8484 (pm20) REVERT: A 316 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9008 (tp30) REVERT: A 331 MET cc_start: 0.8128 (ptm) cc_final: 0.7660 (ptm) REVERT: B 34 ASP cc_start: 0.7956 (p0) cc_final: 0.6712 (p0) REVERT: B 45 GLN cc_start: 0.9089 (tt0) cc_final: 0.8811 (tm-30) REVERT: B 46 ASN cc_start: 0.9216 (m110) cc_final: 0.8998 (m110) REVERT: B 67 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8931 (mp10) REVERT: B 106 VAL cc_start: 0.7629 (m) cc_final: 0.7008 (p) REVERT: B 117 GLN cc_start: 0.8965 (tt0) cc_final: 0.8606 (pt0) REVERT: B 127 PHE cc_start: 0.8536 (t80) cc_final: 0.8273 (t80) REVERT: C 1 MET cc_start: 0.6108 (tpt) cc_final: 0.5490 (ptt) REVERT: C 6 GLN cc_start: 0.8875 (tt0) cc_final: 0.8451 (tt0) REVERT: C 8 MET cc_start: 0.9057 (mtt) cc_final: 0.8817 (mpp) REVERT: C 14 ASP cc_start: 0.9215 (p0) cc_final: 0.8655 (p0) REVERT: C 79 TRP cc_start: 0.9082 (t-100) cc_final: 0.8699 (m100) REVERT: C 101 ASP cc_start: 0.8578 (t0) cc_final: 0.8328 (p0) REVERT: C 105 GLN cc_start: 0.8904 (mt0) cc_final: 0.8521 (mt0) REVERT: C 107 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9105 (mp) REVERT: C 109 LEU cc_start: 0.8705 (mt) cc_final: 0.8472 (tp) REVERT: D 193 GLU cc_start: 0.9330 (tp30) cc_final: 0.9094 (tp30) REVERT: D 202 PHE cc_start: 0.8565 (t80) cc_final: 0.8364 (t80) REVERT: D 207 LEU cc_start: 0.8436 (mm) cc_final: 0.8209 (pt) REVERT: D 248 ARG cc_start: 0.8226 (mtp85) cc_final: 0.7802 (mtp180) REVERT: D 252 ARG cc_start: 0.9449 (ttp80) cc_final: 0.9233 (ttp80) REVERT: D 282 GLU cc_start: 0.8905 (tp30) cc_final: 0.8484 (pm20) REVERT: D 316 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9006 (tp30) REVERT: D 331 MET cc_start: 0.8129 (ptm) cc_final: 0.7661 (ptm) REVERT: E 34 ASP cc_start: 0.7950 (p0) cc_final: 0.6705 (p0) REVERT: E 45 GLN cc_start: 0.9091 (tt0) cc_final: 0.8813 (tm-30) REVERT: E 46 ASN cc_start: 0.9213 (m110) cc_final: 0.8997 (m110) REVERT: E 67 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8931 (mp10) REVERT: E 106 VAL cc_start: 0.7630 (m) cc_final: 0.7010 (p) REVERT: E 117 GLN cc_start: 0.8965 (tt0) cc_final: 0.8605 (pt0) REVERT: E 127 PHE cc_start: 0.8534 (t80) cc_final: 0.8271 (t80) REVERT: F 1 MET cc_start: 0.6109 (tpt) cc_final: 0.5488 (ptt) REVERT: F 6 GLN cc_start: 0.8877 (tt0) cc_final: 0.8453 (tt0) REVERT: F 8 MET cc_start: 0.9059 (mtt) cc_final: 0.8819 (mpp) REVERT: F 14 ASP cc_start: 0.9215 (p0) cc_final: 0.8656 (p0) REVERT: F 79 TRP cc_start: 0.9082 (t-100) cc_final: 0.8696 (m100) REVERT: F 101 ASP cc_start: 0.8580 (t0) cc_final: 0.8330 (p0) REVERT: F 105 GLN cc_start: 0.8906 (mt0) cc_final: 0.8524 (mt0) REVERT: F 107 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9105 (mp) REVERT: F 109 LEU cc_start: 0.8706 (mt) cc_final: 0.8472 (tp) REVERT: G 193 GLU cc_start: 0.9332 (tp30) cc_final: 0.9096 (tp30) REVERT: G 207 LEU cc_start: 0.8437 (mm) cc_final: 0.8209 (pt) REVERT: G 248 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7802 (mtp180) REVERT: G 252 ARG cc_start: 0.9449 (ttp80) cc_final: 0.9232 (ttp80) REVERT: G 282 GLU cc_start: 0.8906 (tp30) cc_final: 0.8484 (pm20) REVERT: G 316 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9005 (tp30) REVERT: G 331 MET cc_start: 0.8127 (ptm) cc_final: 0.7656 (ptm) REVERT: H 34 ASP cc_start: 0.7951 (p0) cc_final: 0.6707 (p0) REVERT: H 45 GLN cc_start: 0.9089 (tt0) cc_final: 0.8813 (tm-30) REVERT: H 46 ASN cc_start: 0.9215 (m110) cc_final: 0.8998 (m110) REVERT: H 67 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.8929 (mp10) REVERT: H 106 VAL cc_start: 0.7632 (m) cc_final: 0.7012 (p) REVERT: H 117 GLN cc_start: 0.8964 (tt0) cc_final: 0.8606 (pt0) REVERT: H 127 PHE cc_start: 0.8532 (t80) cc_final: 0.8269 (t80) REVERT: I 1 MET cc_start: 0.6111 (tpt) cc_final: 0.5491 (ptt) REVERT: I 6 GLN cc_start: 0.8877 (tt0) cc_final: 0.8454 (tt0) REVERT: I 8 MET cc_start: 0.9060 (mtt) cc_final: 0.8821 (mpp) REVERT: I 14 ASP cc_start: 0.9213 (p0) cc_final: 0.8651 (p0) REVERT: I 79 TRP cc_start: 0.9083 (t-100) cc_final: 0.8696 (m100) REVERT: I 101 ASP cc_start: 0.8580 (t0) cc_final: 0.8329 (p0) REVERT: I 105 GLN cc_start: 0.8905 (mt0) cc_final: 0.8523 (mt0) REVERT: I 107 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9105 (mp) REVERT: I 109 LEU cc_start: 0.8705 (mt) cc_final: 0.8472 (tp) REVERT: J 193 GLU cc_start: 0.9332 (tp30) cc_final: 0.9095 (tp30) REVERT: J 207 LEU cc_start: 0.8439 (mm) cc_final: 0.8211 (pt) REVERT: J 248 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7803 (mtp180) REVERT: J 252 ARG cc_start: 0.9447 (ttp80) cc_final: 0.9232 (ttp80) REVERT: J 282 GLU cc_start: 0.8906 (tp30) cc_final: 0.8483 (pm20) REVERT: J 316 GLU cc_start: 0.9291 (mt-10) cc_final: 0.9007 (tp30) REVERT: J 331 MET cc_start: 0.8129 (ptm) cc_final: 0.7661 (ptm) REVERT: K 34 ASP cc_start: 0.7952 (p0) cc_final: 0.6707 (p0) REVERT: K 45 GLN cc_start: 0.9092 (tt0) cc_final: 0.8814 (tm-30) REVERT: K 46 ASN cc_start: 0.9217 (m110) cc_final: 0.9000 (m110) REVERT: K 67 GLN cc_start: 0.9236 (OUTLIER) cc_final: 0.8930 (mp10) REVERT: K 106 VAL cc_start: 0.7627 (m) cc_final: 0.7009 (p) REVERT: K 117 GLN cc_start: 0.8964 (tt0) cc_final: 0.8606 (pt0) REVERT: K 127 PHE cc_start: 0.8535 (t80) cc_final: 0.8270 (t80) REVERT: L 1 MET cc_start: 0.6108 (tpt) cc_final: 0.5487 (ptt) REVERT: L 6 GLN cc_start: 0.8879 (tt0) cc_final: 0.8454 (tt0) REVERT: L 8 MET cc_start: 0.9061 (mtt) cc_final: 0.8820 (mpp) REVERT: L 14 ASP cc_start: 0.9215 (p0) cc_final: 0.8655 (p0) REVERT: L 79 TRP cc_start: 0.9084 (t-100) cc_final: 0.8696 (m100) REVERT: L 101 ASP cc_start: 0.8577 (t0) cc_final: 0.8329 (p0) REVERT: L 105 GLN cc_start: 0.8903 (mt0) cc_final: 0.8521 (mt0) REVERT: L 107 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9107 (mp) REVERT: L 109 LEU cc_start: 0.8705 (mt) cc_final: 0.8471 (tp) outliers start: 16 outliers final: 4 residues processed: 628 average time/residue: 0.3293 time to fit residues: 282.9830 Evaluate side-chains 412 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 400 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain F residue 102 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain H residue 67 GLN Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain K residue 67 GLN Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 102 optimal weight: 0.8980 chunk 159 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS B 8 GLN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN D 227 HIS E 8 GLN ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN G 227 HIS H 8 GLN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 227 HIS K 8 GLN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15648 Z= 0.214 Angle : 0.740 9.985 21132 Z= 0.370 Chirality : 0.052 0.270 2104 Planarity : 0.006 0.063 2728 Dihedral : 8.249 84.723 2032 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 3.46 % Allowed : 13.83 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -3.88 (0.18), residues: 1752 helix: -3.00 (0.17), residues: 532 sheet: -2.49 (0.25), residues: 384 loop : -2.19 (0.21), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 174 HIS 0.005 0.001 HIS C 43 PHE 0.018 0.002 PHE H 18 TYR 0.023 0.001 TYR B 29 ARG 0.006 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 428 time to evaluate : 1.916 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: symmetry clash revert: symmetry clash REVERT: A 193 GLU cc_start: 0.9401 (tp30) cc_final: 0.9183 (tp30) REVERT: A 202 PHE cc_start: 0.8547 (t80) cc_final: 0.8341 (t80) REVERT: A 207 LEU cc_start: 0.8504 (mm) cc_final: 0.8263 (pt) REVERT: A 215 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8682 (mp0) REVERT: A 252 ARG cc_start: 0.9308 (ttp80) cc_final: 0.9046 (ttp80) REVERT: A 282 GLU cc_start: 0.8793 (tp30) cc_final: 0.8476 (pm20) REVERT: A 331 MET cc_start: 0.7723 (ptm) cc_final: 0.7473 (ptm) REVERT: B 34 ASP cc_start: 0.7863 (p0) cc_final: 0.6699 (p0) REVERT: B 46 ASN cc_start: 0.9345 (m110) cc_final: 0.9093 (m110) REVERT: B 106 VAL cc_start: 0.7852 (m) cc_final: 0.7604 (p) REVERT: B 117 GLN cc_start: 0.9003 (tt0) cc_final: 0.8705 (pt0) REVERT: B 127 PHE cc_start: 0.8618 (t80) cc_final: 0.8384 (t80) REVERT: B 133 GLN cc_start: 0.7236 (mp10) cc_final: 0.6698 (mp10) REVERT: B 141 GLN cc_start: 0.8890 (tt0) cc_final: 0.8636 (mp10) REVERT: B 149 ARG cc_start: 0.7927 (ttt90) cc_final: 0.7589 (ttp80) REVERT: C 1 MET cc_start: 0.6715 (tpt) cc_final: 0.5765 (ptm) REVERT: C 21 TRP cc_start: 0.9164 (t-100) cc_final: 0.8847 (t-100) REVERT: C 63 LYS cc_start: 0.7756 (ptpp) cc_final: 0.7546 (ptpp) REVERT: C 91 LYS cc_start: 0.7532 (tptt) cc_final: 0.7120 (mttt) REVERT: C 105 GLN cc_start: 0.8753 (mt0) cc_final: 0.8499 (mt0) REVERT: D 193 GLU cc_start: 0.9401 (tp30) cc_final: 0.9183 (tp30) REVERT: D 207 LEU cc_start: 0.8504 (mm) cc_final: 0.8262 (pt) REVERT: D 215 GLU cc_start: 0.8999 (mm-30) cc_final: 0.8690 (mp0) REVERT: D 252 ARG cc_start: 0.9308 (ttp80) cc_final: 0.9045 (ttp80) REVERT: D 282 GLU cc_start: 0.8793 (tp30) cc_final: 0.8475 (pm20) REVERT: D 331 MET cc_start: 0.7725 (ptm) cc_final: 0.7470 (ptm) REVERT: E 34 ASP cc_start: 0.7864 (p0) cc_final: 0.6700 (p0) REVERT: E 46 ASN cc_start: 0.9348 (m110) cc_final: 0.9095 (m110) REVERT: E 106 VAL cc_start: 0.7850 (m) cc_final: 0.7604 (p) REVERT: E 117 GLN cc_start: 0.9002 (tt0) cc_final: 0.8705 (pt0) REVERT: E 127 PHE cc_start: 0.8620 (t80) cc_final: 0.8386 (t80) REVERT: E 133 GLN cc_start: 0.7233 (mp10) cc_final: 0.6696 (mp10) REVERT: E 141 GLN cc_start: 0.8891 (tt0) cc_final: 0.8637 (mp10) REVERT: E 149 ARG cc_start: 0.7924 (ttt90) cc_final: 0.7587 (ttp80) REVERT: F 1 MET cc_start: 0.6717 (tpt) cc_final: 0.5763 (ptm) REVERT: F 21 TRP cc_start: 0.9163 (t-100) cc_final: 0.8848 (t-100) REVERT: F 63 LYS cc_start: 0.7752 (ptpp) cc_final: 0.7542 (ptpp) REVERT: F 91 LYS cc_start: 0.7532 (tptt) cc_final: 0.7123 (mttt) REVERT: F 105 GLN cc_start: 0.8754 (mt0) cc_final: 0.8499 (mt0) REVERT: G 193 GLU cc_start: 0.9402 (tp30) cc_final: 0.9184 (tp30) REVERT: G 202 PHE cc_start: 0.8546 (t80) cc_final: 0.8339 (t80) REVERT: G 207 LEU cc_start: 0.8503 (mm) cc_final: 0.8262 (pt) REVERT: G 215 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8684 (mp0) REVERT: G 252 ARG cc_start: 0.9308 (ttp80) cc_final: 0.9045 (ttp80) REVERT: G 282 GLU cc_start: 0.8792 (tp30) cc_final: 0.8476 (pm20) REVERT: G 331 MET cc_start: 0.7723 (ptm) cc_final: 0.7469 (ptm) REVERT: H 34 ASP cc_start: 0.7867 (p0) cc_final: 0.6703 (p0) REVERT: H 46 ASN cc_start: 0.9345 (m110) cc_final: 0.9094 (m110) REVERT: H 106 VAL cc_start: 0.7854 (m) cc_final: 0.7605 (p) REVERT: H 117 GLN cc_start: 0.9002 (tt0) cc_final: 0.8706 (pt0) REVERT: H 127 PHE cc_start: 0.8620 (t80) cc_final: 0.8386 (t80) REVERT: H 133 GLN cc_start: 0.7236 (mp10) cc_final: 0.6699 (mp10) REVERT: H 141 GLN cc_start: 0.8893 (tt0) cc_final: 0.8638 (mp10) REVERT: H 149 ARG cc_start: 0.7926 (ttt90) cc_final: 0.7589 (ttp80) REVERT: I 1 MET cc_start: 0.6717 (tpt) cc_final: 0.5766 (ptm) REVERT: I 21 TRP cc_start: 0.9162 (t-100) cc_final: 0.8847 (t-100) REVERT: I 63 LYS cc_start: 0.7755 (ptpp) cc_final: 0.7546 (ptpp) REVERT: I 91 LYS cc_start: 0.7530 (tptt) cc_final: 0.7121 (mttt) REVERT: I 105 GLN cc_start: 0.8753 (mt0) cc_final: 0.8498 (mt0) REVERT: J 193 GLU cc_start: 0.9401 (tp30) cc_final: 0.9183 (tp30) REVERT: J 202 PHE cc_start: 0.8543 (t80) cc_final: 0.8336 (t80) REVERT: J 207 LEU cc_start: 0.8502 (mm) cc_final: 0.8261 (pt) REVERT: J 215 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8682 (mp0) REVERT: J 252 ARG cc_start: 0.9306 (ttp80) cc_final: 0.9044 (ttp80) REVERT: J 282 GLU cc_start: 0.8794 (tp30) cc_final: 0.8476 (pm20) REVERT: J 331 MET cc_start: 0.7727 (ptm) cc_final: 0.7473 (ptm) REVERT: K 34 ASP cc_start: 0.7861 (p0) cc_final: 0.6698 (p0) REVERT: K 46 ASN cc_start: 0.9347 (m110) cc_final: 0.9095 (m110) REVERT: K 106 VAL cc_start: 0.7853 (m) cc_final: 0.7603 (p) REVERT: K 117 GLN cc_start: 0.9002 (tt0) cc_final: 0.8704 (pt0) REVERT: K 127 PHE cc_start: 0.8618 (t80) cc_final: 0.8381 (t80) REVERT: K 133 GLN cc_start: 0.7235 (mp10) cc_final: 0.6697 (mp10) REVERT: K 141 GLN cc_start: 0.8892 (tt0) cc_final: 0.8637 (mp10) REVERT: K 149 ARG cc_start: 0.7925 (ttt90) cc_final: 0.7587 (ttp80) REVERT: L 1 MET cc_start: 0.6718 (tpt) cc_final: 0.5765 (ptm) REVERT: L 21 TRP cc_start: 0.9165 (t-100) cc_final: 0.8848 (t-100) REVERT: L 63 LYS cc_start: 0.7752 (ptpp) cc_final: 0.7543 (ptpp) REVERT: L 91 LYS cc_start: 0.7531 (tptt) cc_final: 0.7121 (mttt) REVERT: L 105 GLN cc_start: 0.8754 (mt0) cc_final: 0.8499 (mt0) outliers start: 56 outliers final: 28 residues processed: 460 average time/residue: 0.2900 time to fit residues: 190.0044 Evaluate side-chains 380 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 352 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 78 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN D 227 HIS ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN G 227 HIS ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 227 HIS ** J 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 15648 Z= 0.371 Angle : 0.765 11.144 21132 Z= 0.387 Chirality : 0.052 0.221 2104 Planarity : 0.005 0.044 2728 Dihedral : 6.173 23.236 2004 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.73 % Favored : 89.27 % Rotamer: Outliers : 4.69 % Allowed : 16.79 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -3.56 (0.19), residues: 1752 helix: -2.50 (0.19), residues: 588 sheet: -1.92 (0.26), residues: 360 loop : -2.35 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 5 HIS 0.006 0.001 HIS D 203 PHE 0.019 0.003 PHE B 17 TYR 0.017 0.002 TYR A 308 ARG 0.004 0.001 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 312 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.8799 (mm) cc_final: 0.8351 (pt) REVERT: A 215 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8700 (mp0) REVERT: A 282 GLU cc_start: 0.8827 (tp30) cc_final: 0.8531 (pm20) REVERT: B 46 ASN cc_start: 0.9235 (m110) cc_final: 0.9018 (m110) REVERT: B 117 GLN cc_start: 0.9101 (tt0) cc_final: 0.8855 (pt0) REVERT: B 149 ARG cc_start: 0.8097 (ttt90) cc_final: 0.7706 (ttp80) REVERT: C 1 MET cc_start: 0.6684 (tpt) cc_final: 0.5849 (ptt) REVERT: C 91 LYS cc_start: 0.7983 (tptt) cc_final: 0.7522 (mtmt) REVERT: C 107 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.9005 (mp) REVERT: D 207 LEU cc_start: 0.8808 (mm) cc_final: 0.8359 (pt) REVERT: D 215 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8712 (mp0) REVERT: D 282 GLU cc_start: 0.8829 (tp30) cc_final: 0.8532 (pm20) REVERT: E 46 ASN cc_start: 0.9238 (m110) cc_final: 0.9021 (m110) REVERT: E 117 GLN cc_start: 0.9101 (tt0) cc_final: 0.8856 (pt0) REVERT: E 149 ARG cc_start: 0.8096 (ttt90) cc_final: 0.7703 (ttp80) REVERT: F 1 MET cc_start: 0.6687 (tpt) cc_final: 0.5849 (ptt) REVERT: F 91 LYS cc_start: 0.7983 (tptt) cc_final: 0.7524 (mtmt) REVERT: F 107 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.9005 (mp) REVERT: G 207 LEU cc_start: 0.8800 (mm) cc_final: 0.8351 (pt) REVERT: G 215 GLU cc_start: 0.9012 (mm-30) cc_final: 0.8701 (mp0) REVERT: G 282 GLU cc_start: 0.8827 (tp30) cc_final: 0.8532 (pm20) REVERT: H 46 ASN cc_start: 0.9235 (m110) cc_final: 0.9019 (m110) REVERT: H 117 GLN cc_start: 0.9101 (tt0) cc_final: 0.8855 (pt0) REVERT: H 149 ARG cc_start: 0.8097 (ttt90) cc_final: 0.7705 (ttp80) REVERT: I 1 MET cc_start: 0.6684 (tpt) cc_final: 0.5850 (ptt) REVERT: I 91 LYS cc_start: 0.7982 (tptt) cc_final: 0.7522 (mtmt) REVERT: I 107 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.9004 (mp) REVERT: J 207 LEU cc_start: 0.8800 (mm) cc_final: 0.8351 (pt) REVERT: J 215 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8701 (mp0) REVERT: J 282 GLU cc_start: 0.8828 (tp30) cc_final: 0.8531 (pm20) REVERT: K 46 ASN cc_start: 0.9237 (m110) cc_final: 0.9021 (m110) REVERT: K 117 GLN cc_start: 0.9100 (tt0) cc_final: 0.8855 (pt0) REVERT: K 149 ARG cc_start: 0.8097 (ttt90) cc_final: 0.7705 (ttp80) REVERT: L 1 MET cc_start: 0.6686 (tpt) cc_final: 0.5851 (ptt) REVERT: L 91 LYS cc_start: 0.7986 (tptt) cc_final: 0.7527 (mtmt) REVERT: L 107 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.9006 (mp) outliers start: 76 outliers final: 32 residues processed: 352 average time/residue: 0.2441 time to fit residues: 129.2411 Evaluate side-chains 312 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 276 time to evaluate : 1.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 160 optimal weight: 0.3980 chunk 170 optimal weight: 4.9990 chunk 152 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 141 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN D 227 HIS ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN G 227 HIS ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 227 HIS ** J 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15648 Z= 0.175 Angle : 0.687 10.055 21132 Z= 0.334 Chirality : 0.048 0.218 2104 Planarity : 0.004 0.045 2728 Dihedral : 5.695 21.781 2004 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 4.20 % Allowed : 17.04 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -3.10 (0.19), residues: 1752 helix: -2.06 (0.20), residues: 596 sheet: -1.46 (0.27), residues: 360 loop : -2.25 (0.22), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 5 HIS 0.004 0.001 HIS C 43 PHE 0.024 0.002 PHE E 127 TYR 0.021 0.001 TYR K 29 ARG 0.004 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 324 time to evaluate : 1.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.8727 (mm) cc_final: 0.8385 (pt) REVERT: A 215 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8736 (mp0) REVERT: A 282 GLU cc_start: 0.8840 (tp30) cc_final: 0.8482 (pm20) REVERT: B 84 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7244 (pm20) REVERT: B 117 GLN cc_start: 0.9072 (tt0) cc_final: 0.8722 (pt0) REVERT: B 149 ARG cc_start: 0.7976 (ttt90) cc_final: 0.7564 (ttp80) REVERT: C 1 MET cc_start: 0.6918 (tpt) cc_final: 0.5813 (ptt) REVERT: C 91 LYS cc_start: 0.7985 (tptt) cc_final: 0.7567 (mtmt) REVERT: C 107 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9035 (mp) REVERT: D 207 LEU cc_start: 0.8793 (mm) cc_final: 0.8404 (pt) REVERT: D 215 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8733 (mp0) REVERT: D 282 GLU cc_start: 0.8840 (tp30) cc_final: 0.8482 (pm20) REVERT: E 84 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: E 117 GLN cc_start: 0.9070 (tt0) cc_final: 0.8723 (pt0) REVERT: E 149 ARG cc_start: 0.7973 (ttt90) cc_final: 0.7561 (ttp80) REVERT: F 1 MET cc_start: 0.6918 (tpt) cc_final: 0.5808 (ptt) REVERT: F 91 LYS cc_start: 0.7985 (tptt) cc_final: 0.7568 (mtmt) REVERT: F 107 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.9033 (mp) REVERT: G 207 LEU cc_start: 0.8729 (mm) cc_final: 0.8385 (pt) REVERT: G 215 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8737 (mp0) REVERT: G 282 GLU cc_start: 0.8839 (tp30) cc_final: 0.8482 (pm20) REVERT: H 84 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7246 (pm20) REVERT: H 117 GLN cc_start: 0.9071 (tt0) cc_final: 0.8722 (pt0) REVERT: H 149 ARG cc_start: 0.7975 (ttt90) cc_final: 0.7563 (ttp80) REVERT: I 1 MET cc_start: 0.6918 (tpt) cc_final: 0.5809 (ptt) REVERT: I 91 LYS cc_start: 0.7985 (tptt) cc_final: 0.7568 (mtmt) REVERT: I 107 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.9033 (mp) REVERT: J 207 LEU cc_start: 0.8726 (mm) cc_final: 0.8384 (pt) REVERT: J 215 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8737 (mp0) REVERT: J 282 GLU cc_start: 0.8840 (tp30) cc_final: 0.8482 (pm20) REVERT: K 84 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7243 (pm20) REVERT: K 117 GLN cc_start: 0.9071 (tt0) cc_final: 0.8721 (pt0) REVERT: K 149 ARG cc_start: 0.7974 (ttt90) cc_final: 0.7562 (ttp80) REVERT: L 1 MET cc_start: 0.6918 (tpt) cc_final: 0.5809 (ptt) REVERT: L 91 LYS cc_start: 0.7987 (tptt) cc_final: 0.7570 (mtmt) REVERT: L 107 ILE cc_start: 0.9234 (OUTLIER) cc_final: 0.9034 (mp) outliers start: 68 outliers final: 28 residues processed: 376 average time/residue: 0.2204 time to fit residues: 127.4543 Evaluate side-chains 344 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 308 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 363 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 152 optimal weight: 7.9990 chunk 42 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS B 14 ASN B 63 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN C 158 GLN D 227 HIS E 14 ASN E 63 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN F 158 GLN G 227 HIS H 14 ASN H 63 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN I 158 GLN J 227 HIS K 14 ASN K 63 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN L 158 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.4557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.085 15648 Z= 0.545 Angle : 0.853 8.633 21132 Z= 0.439 Chirality : 0.055 0.258 2104 Planarity : 0.006 0.043 2728 Dihedral : 6.227 23.853 2004 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 5.68 % Allowed : 19.75 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -3.19 (0.19), residues: 1752 helix: -1.92 (0.19), residues: 600 sheet: -1.57 (0.28), residues: 352 loop : -2.46 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 277 HIS 0.008 0.002 HIS A 203 PHE 0.022 0.003 PHE E 44 TYR 0.022 0.003 TYR C 40 ARG 0.005 0.001 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 271 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 117 GLN cc_start: 0.9246 (tt0) cc_final: 0.8808 (pt0) REVERT: B 122 MET cc_start: 0.8071 (mmm) cc_final: 0.7870 (mmm) REVERT: B 141 GLN cc_start: 0.8965 (tt0) cc_final: 0.8574 (mp10) REVERT: C 1 MET cc_start: 0.6668 (tpt) cc_final: 0.5867 (ptt) REVERT: E 117 GLN cc_start: 0.9245 (tt0) cc_final: 0.8808 (pt0) REVERT: E 141 GLN cc_start: 0.8964 (tt0) cc_final: 0.8573 (mp10) REVERT: F 1 MET cc_start: 0.6668 (tpt) cc_final: 0.5862 (ptt) REVERT: H 117 GLN cc_start: 0.9245 (tt0) cc_final: 0.8808 (pt0) REVERT: H 122 MET cc_start: 0.8076 (mmm) cc_final: 0.7875 (mmm) REVERT: H 141 GLN cc_start: 0.8965 (tt0) cc_final: 0.8573 (mp10) REVERT: I 1 MET cc_start: 0.6670 (tpt) cc_final: 0.5867 (ptt) REVERT: K 117 GLN cc_start: 0.9244 (tt0) cc_final: 0.8807 (pt0) REVERT: K 122 MET cc_start: 0.8078 (mmm) cc_final: 0.7877 (mmm) REVERT: K 141 GLN cc_start: 0.8966 (tt0) cc_final: 0.8574 (mp10) REVERT: L 1 MET cc_start: 0.6666 (tpt) cc_final: 0.5866 (ptt) outliers start: 92 outliers final: 55 residues processed: 331 average time/residue: 0.2244 time to fit residues: 115.5793 Evaluate side-chains 290 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 235 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 347 ASP Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 291 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 347 ASP Chi-restraints excluded: chain G residue 363 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 347 ASP Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 98 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 41 optimal weight: 0.2980 chunk 170 optimal weight: 0.9990 chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN C 3 ASN C 19 ASN C 158 GLN D 227 HIS ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN E 134 GLN F 3 ASN F 19 ASN F 158 GLN G 227 HIS ** G 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN I 3 ASN I 19 ASN I 158 GLN J 227 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 GLN L 3 ASN L 19 ASN L 158 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15648 Z= 0.186 Angle : 0.703 10.032 21132 Z= 0.343 Chirality : 0.050 0.226 2104 Planarity : 0.005 0.045 2728 Dihedral : 5.662 21.509 2004 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 3.02 % Allowed : 21.48 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -2.86 (0.19), residues: 1752 helix: -1.56 (0.20), residues: 604 sheet: -1.34 (0.28), residues: 360 loop : -2.36 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 277 HIS 0.006 0.001 HIS F 43 PHE 0.015 0.001 PHE G 202 TYR 0.017 0.001 TYR C 40 ARG 0.003 0.000 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 311 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.8881 (tp30) cc_final: 0.8490 (pm20) REVERT: A 299 LEU cc_start: 0.9492 (tt) cc_final: 0.9292 (tt) REVERT: B 117 GLN cc_start: 0.9062 (tt0) cc_final: 0.8668 (pt0) REVERT: B 122 MET cc_start: 0.8036 (mmm) cc_final: 0.7797 (mmm) REVERT: B 128 ASP cc_start: 0.8000 (t0) cc_final: 0.7623 (t70) REVERT: B 141 GLN cc_start: 0.8954 (tt0) cc_final: 0.8562 (mp10) REVERT: C 1 MET cc_start: 0.7119 (tpt) cc_final: 0.5687 (ptt) REVERT: C 107 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9008 (mp) REVERT: D 282 GLU cc_start: 0.8880 (tp30) cc_final: 0.8489 (pm20) REVERT: D 299 LEU cc_start: 0.9489 (tt) cc_final: 0.9288 (tt) REVERT: E 117 GLN cc_start: 0.9065 (tt0) cc_final: 0.8678 (pt0) REVERT: E 128 ASP cc_start: 0.7998 (t0) cc_final: 0.7622 (t70) REVERT: E 141 GLN cc_start: 0.8957 (tt0) cc_final: 0.8564 (mp10) REVERT: F 1 MET cc_start: 0.7116 (tpt) cc_final: 0.5685 (ptt) REVERT: F 107 ILE cc_start: 0.9265 (OUTLIER) cc_final: 0.9008 (mp) REVERT: G 282 GLU cc_start: 0.8882 (tp30) cc_final: 0.8491 (pm20) REVERT: G 299 LEU cc_start: 0.9489 (tt) cc_final: 0.9288 (tt) REVERT: H 117 GLN cc_start: 0.9062 (tt0) cc_final: 0.8669 (pt0) REVERT: H 122 MET cc_start: 0.8036 (mmm) cc_final: 0.7798 (mmm) REVERT: H 128 ASP cc_start: 0.7999 (t0) cc_final: 0.7623 (t70) REVERT: H 141 GLN cc_start: 0.8955 (tt0) cc_final: 0.8562 (mp10) REVERT: I 1 MET cc_start: 0.7115 (tpt) cc_final: 0.5686 (ptt) REVERT: I 107 ILE cc_start: 0.9263 (OUTLIER) cc_final: 0.9005 (mp) REVERT: J 282 GLU cc_start: 0.8883 (tp30) cc_final: 0.8491 (pm20) REVERT: J 299 LEU cc_start: 0.9492 (tt) cc_final: 0.9291 (tt) REVERT: K 117 GLN cc_start: 0.9060 (tt0) cc_final: 0.8667 (pt0) REVERT: K 122 MET cc_start: 0.8040 (mmm) cc_final: 0.7802 (mmm) REVERT: K 128 ASP cc_start: 0.7998 (t0) cc_final: 0.7622 (t70) REVERT: K 141 GLN cc_start: 0.8955 (tt0) cc_final: 0.8562 (mp10) REVERT: L 1 MET cc_start: 0.7118 (tpt) cc_final: 0.5688 (ptt) REVERT: L 107 ILE cc_start: 0.9264 (OUTLIER) cc_final: 0.9008 (mp) outliers start: 49 outliers final: 40 residues processed: 340 average time/residue: 0.2079 time to fit residues: 112.9397 Evaluate side-chains 315 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 271 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 363 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 143 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 104 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS B 63 ASN C 3 ASN C 158 GLN D 227 HIS E 63 ASN F 3 ASN F 158 GLN G 227 HIS H 63 ASN I 3 ASN I 158 GLN J 227 HIS K 63 ASN L 3 ASN L 158 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15648 Z= 0.241 Angle : 0.723 10.253 21132 Z= 0.347 Chirality : 0.052 0.295 2104 Planarity : 0.005 0.045 2728 Dihedral : 5.509 20.513 2004 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.07 % Allowed : 22.10 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -2.58 (0.20), residues: 1752 helix: -1.45 (0.21), residues: 604 sheet: -1.18 (0.27), residues: 360 loop : -2.10 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 277 HIS 0.004 0.001 HIS I 43 PHE 0.015 0.002 PHE D 202 TYR 0.010 0.001 TYR I 40 ARG 0.003 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 280 time to evaluate : 1.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.8853 (tp30) cc_final: 0.8450 (pm20) REVERT: B 117 GLN cc_start: 0.9093 (tt0) cc_final: 0.8701 (pt0) REVERT: B 128 ASP cc_start: 0.7965 (t0) cc_final: 0.7593 (t70) REVERT: B 141 GLN cc_start: 0.8948 (tt0) cc_final: 0.8553 (mp10) REVERT: C 1 MET cc_start: 0.7128 (tpt) cc_final: 0.5696 (ptt) REVERT: C 107 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9079 (mp) REVERT: D 282 GLU cc_start: 0.8853 (tp30) cc_final: 0.8450 (pm20) REVERT: E 117 GLN cc_start: 0.9095 (tt0) cc_final: 0.8704 (pt0) REVERT: E 128 ASP cc_start: 0.7965 (t0) cc_final: 0.7592 (t70) REVERT: E 141 GLN cc_start: 0.8949 (tt0) cc_final: 0.8553 (mp10) REVERT: F 1 MET cc_start: 0.7128 (tpt) cc_final: 0.5693 (ptt) REVERT: F 107 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9077 (mp) REVERT: G 282 GLU cc_start: 0.8854 (tp30) cc_final: 0.8451 (pm20) REVERT: H 117 GLN cc_start: 0.9093 (tt0) cc_final: 0.8702 (pt0) REVERT: H 128 ASP cc_start: 0.7967 (t0) cc_final: 0.7594 (t70) REVERT: H 141 GLN cc_start: 0.8949 (tt0) cc_final: 0.8553 (mp10) REVERT: I 1 MET cc_start: 0.7127 (tpt) cc_final: 0.5693 (ptt) REVERT: I 107 ILE cc_start: 0.9315 (OUTLIER) cc_final: 0.9078 (mp) REVERT: J 282 GLU cc_start: 0.8853 (tp30) cc_final: 0.8450 (pm20) REVERT: K 117 GLN cc_start: 0.9092 (tt0) cc_final: 0.8700 (pt0) REVERT: K 128 ASP cc_start: 0.7962 (t0) cc_final: 0.7593 (t70) REVERT: K 141 GLN cc_start: 0.8948 (tt0) cc_final: 0.8554 (mp10) REVERT: L 1 MET cc_start: 0.7129 (tpt) cc_final: 0.5696 (ptt) REVERT: L 107 ILE cc_start: 0.9316 (OUTLIER) cc_final: 0.9079 (mp) outliers start: 66 outliers final: 47 residues processed: 320 average time/residue: 0.2089 time to fit residues: 107.1443 Evaluate side-chains 315 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 264 time to evaluate : 1.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 363 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 63 ASN Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 107 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 133 optimal weight: 1.9990 chunk 154 optimal weight: 0.1980 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 63 ASN F 3 ASN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS H 63 ASN I 3 ASN ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 HIS ** J 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15648 Z= 0.207 Angle : 0.729 11.668 21132 Z= 0.345 Chirality : 0.052 0.289 2104 Planarity : 0.004 0.045 2728 Dihedral : 5.408 20.169 2004 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 15.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 4.32 % Allowed : 22.04 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -2.44 (0.20), residues: 1752 helix: -1.33 (0.21), residues: 604 sheet: -1.09 (0.27), residues: 360 loop : -2.01 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 277 HIS 0.004 0.001 HIS I 43 PHE 0.017 0.002 PHE A 202 TYR 0.015 0.001 TYR I 40 ARG 0.003 0.000 ARG K 33 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 303 time to evaluate : 1.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.8891 (tp30) cc_final: 0.8473 (pm20) REVERT: B 117 GLN cc_start: 0.9079 (tt0) cc_final: 0.8706 (pt0) REVERT: B 128 ASP cc_start: 0.7871 (t0) cc_final: 0.7534 (t70) REVERT: B 141 GLN cc_start: 0.8954 (tt0) cc_final: 0.8573 (mp10) REVERT: C 107 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9090 (mp) REVERT: D 282 GLU cc_start: 0.8888 (tp30) cc_final: 0.8472 (pm20) REVERT: E 117 GLN cc_start: 0.9087 (tt0) cc_final: 0.8716 (pt0) REVERT: E 128 ASP cc_start: 0.7869 (t0) cc_final: 0.7532 (t70) REVERT: E 141 GLN cc_start: 0.8955 (tt0) cc_final: 0.8574 (mp10) REVERT: F 107 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9089 (mp) REVERT: G 282 GLU cc_start: 0.8885 (tp30) cc_final: 0.8469 (pm20) REVERT: H 84 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7213 (pm20) REVERT: H 117 GLN cc_start: 0.9080 (tt0) cc_final: 0.8708 (pt0) REVERT: H 128 ASP cc_start: 0.7870 (t0) cc_final: 0.7530 (t70) REVERT: H 141 GLN cc_start: 0.8955 (tt0) cc_final: 0.8576 (mp10) REVERT: I 107 ILE cc_start: 0.9301 (OUTLIER) cc_final: 0.9089 (mp) REVERT: J 282 GLU cc_start: 0.8892 (tp30) cc_final: 0.8473 (pm20) REVERT: K 117 GLN cc_start: 0.9077 (tt0) cc_final: 0.8706 (pt0) REVERT: K 128 ASP cc_start: 0.7868 (t0) cc_final: 0.7532 (t70) REVERT: K 141 GLN cc_start: 0.8955 (tt0) cc_final: 0.8574 (mp10) REVERT: L 107 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9089 (mp) outliers start: 70 outliers final: 59 residues processed: 350 average time/residue: 0.2150 time to fit residues: 119.7760 Evaluate side-chains 344 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 280 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 363 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 313 ASP Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 78 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 chunk 95 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 157 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 63 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN F 73 HIS ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN I 73 HIS ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 HIS ** J 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN L 73 HIS ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.4789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15648 Z= 0.272 Angle : 0.764 10.592 21132 Z= 0.364 Chirality : 0.053 0.318 2104 Planarity : 0.005 0.045 2728 Dihedral : 5.421 19.287 2004 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 16.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 4.26 % Allowed : 22.72 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -2.39 (0.20), residues: 1752 helix: -1.25 (0.21), residues: 608 sheet: -1.04 (0.27), residues: 360 loop : -2.04 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 277 HIS 0.004 0.001 HIS C 43 PHE 0.016 0.002 PHE D 202 TYR 0.011 0.001 TYR L 40 ARG 0.003 0.000 ARG E 33 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 279 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.8864 (tp30) cc_final: 0.8435 (pm20) REVERT: B 117 GLN cc_start: 0.9170 (tt0) cc_final: 0.8804 (pt0) REVERT: B 128 ASP cc_start: 0.7873 (t0) cc_final: 0.7536 (t70) REVERT: B 141 GLN cc_start: 0.8984 (tt0) cc_final: 0.8576 (mp10) REVERT: C 107 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.9062 (mp) REVERT: D 282 GLU cc_start: 0.8863 (tp30) cc_final: 0.8436 (pm20) REVERT: E 117 GLN cc_start: 0.9173 (tt0) cc_final: 0.8807 (pt0) REVERT: E 128 ASP cc_start: 0.7872 (t0) cc_final: 0.7533 (t70) REVERT: E 141 GLN cc_start: 0.8985 (tt0) cc_final: 0.8578 (mp10) REVERT: F 107 ILE cc_start: 0.9308 (OUTLIER) cc_final: 0.9075 (mp) REVERT: G 282 GLU cc_start: 0.8861 (tp30) cc_final: 0.8432 (pm20) REVERT: H 117 GLN cc_start: 0.9172 (tt0) cc_final: 0.8805 (pt0) REVERT: H 128 ASP cc_start: 0.7876 (t0) cc_final: 0.7539 (t70) REVERT: H 141 GLN cc_start: 0.8984 (tt0) cc_final: 0.8576 (mp10) REVERT: I 107 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.9060 (mp) REVERT: J 282 GLU cc_start: 0.8866 (tp30) cc_final: 0.8435 (pm20) REVERT: K 117 GLN cc_start: 0.9171 (tt0) cc_final: 0.8804 (pt0) REVERT: K 128 ASP cc_start: 0.7871 (t0) cc_final: 0.7535 (t70) REVERT: K 141 GLN cc_start: 0.8984 (tt0) cc_final: 0.8577 (mp10) REVERT: L 107 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9076 (mp) outliers start: 69 outliers final: 60 residues processed: 326 average time/residue: 0.2215 time to fit residues: 116.6265 Evaluate side-chains 326 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 262 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 3 ASN Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 3 ASN Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 363 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 3 ASN Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 313 ASP Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 3 ASN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 175 optimal weight: 2.9990 chunk 161 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS H 63 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 HIS ** J 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15648 Z= 0.258 Angle : 0.778 13.676 21132 Z= 0.367 Chirality : 0.053 0.311 2104 Planarity : 0.005 0.046 2728 Dihedral : 5.397 19.367 2004 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.71 % Favored : 92.29 % Rotamer: Outliers : 4.26 % Allowed : 22.59 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % 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: -2.37 (0.20), residues: 1752 helix: -1.18 (0.21), residues: 608 sheet: -1.06 (0.27), residues: 356 loop : -2.06 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 277 HIS 0.004 0.001 HIS F 43 PHE 0.013 0.002 PHE K 44 TYR 0.013 0.001 TYR F 40 ARG 0.003 0.000 ARG E 33 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3504 Ramachandran restraints generated. 1752 Oldfield, 0 Emsley, 1752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 281 time to evaluate : 1.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 282 GLU cc_start: 0.8867 (tp30) cc_final: 0.8434 (pm20) REVERT: B 117 GLN cc_start: 0.9171 (tt0) cc_final: 0.8804 (pt0) REVERT: B 128 ASP cc_start: 0.7920 (t0) cc_final: 0.7585 (t70) REVERT: B 141 GLN cc_start: 0.8990 (tt0) cc_final: 0.8578 (mp10) REVERT: C 107 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9033 (mp) REVERT: D 282 GLU cc_start: 0.8867 (tp30) cc_final: 0.8434 (pm20) REVERT: E 117 GLN cc_start: 0.9146 (tt0) cc_final: 0.8724 (pt0) REVERT: E 128 ASP cc_start: 0.7922 (t0) cc_final: 0.7586 (t70) REVERT: E 141 GLN cc_start: 0.8991 (tt0) cc_final: 0.8579 (mp10) REVERT: F 107 ILE cc_start: 0.9285 (OUTLIER) cc_final: 0.9034 (mp) REVERT: G 282 GLU cc_start: 0.8864 (tp30) cc_final: 0.8429 (pm20) REVERT: H 117 GLN cc_start: 0.9174 (tt0) cc_final: 0.8807 (pt0) REVERT: H 128 ASP cc_start: 0.7924 (t0) cc_final: 0.7589 (t70) REVERT: H 141 GLN cc_start: 0.8992 (tt0) cc_final: 0.8580 (mp10) REVERT: I 107 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.9044 (mp) REVERT: J 282 GLU cc_start: 0.8868 (tp30) cc_final: 0.8435 (pm20) REVERT: K 117 GLN cc_start: 0.9172 (tt0) cc_final: 0.8805 (pt0) REVERT: K 128 ASP cc_start: 0.7919 (t0) cc_final: 0.7585 (t70) REVERT: K 141 GLN cc_start: 0.8992 (tt0) cc_final: 0.8581 (mp10) REVERT: L 107 ILE cc_start: 0.9286 (OUTLIER) cc_final: 0.9036 (mp) outliers start: 69 outliers final: 60 residues processed: 322 average time/residue: 0.2065 time to fit residues: 106.8081 Evaluate side-chains 340 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 276 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 363 ASP Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 61 ASP Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 107 ILE Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 363 ASP Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 61 ASP Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 218 LEU Chi-restraints excluded: chain G residue 263 LEU Chi-restraints excluded: chain G residue 303 THR Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 363 ASP Chi-restraints excluded: chain H residue 4 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 98 VAL Chi-restraints excluded: chain I residue 107 ILE Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 218 LEU Chi-restraints excluded: chain J residue 263 LEU Chi-restraints excluded: chain J residue 291 LEU Chi-restraints excluded: chain J residue 303 THR Chi-restraints excluded: chain J residue 313 ASP Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 363 ASP Chi-restraints excluded: chain K residue 4 VAL Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 61 ASP Chi-restraints excluded: chain L residue 98 VAL Chi-restraints excluded: chain L residue 107 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 9.9990 chunk 42 optimal weight: 3.9990 chunk 128 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 139 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS H 63 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 HIS ** J 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.120573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.091788 restraints weight = 32847.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.094437 restraints weight = 20405.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.096102 restraints weight = 15548.566| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 15648 Z= 0.310 Angle : 0.932 59.200 21132 Z= 0.492 Chirality : 0.055 0.738 2104 Planarity : 0.005 0.051 2728 Dihedral : 5.448 36.502 2004 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 18.12 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.71 % Favored : 92.24 % Rotamer: Outliers : 3.89 % Allowed : 23.46 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.37 (0.20), residues: 1752 helix: -1.19 (0.21), residues: 608 sheet: -1.06 (0.27), residues: 356 loop : -2.06 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 277 HIS 0.004 0.001 HIS F 27 PHE 0.013 0.002 PHE K 44 TYR 0.009 0.001 TYR G 359 ARG 0.002 0.000 ARG K 33 =============================================================================== Job complete usr+sys time: 3184.77 seconds wall clock time: 58 minutes 45.76 seconds (3525.76 seconds total)