Starting phenix.real_space_refine on Sun Dec 10 18:26:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/12_2023/6nil_9380.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/12_2023/6nil_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_9380/12_2023/6nil_9380.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/12_2023/6nil_9380.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/12_2023/6nil_9380.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nil_9380/12_2023/6nil_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-1.21rc1-5172/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: 7.79, per 1000 atoms: 0.51 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: 5.17 Conformation dependent library (CDL) restraints added in 2.8 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: 1.86 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: 4.22 Time building geometry restraints manager: 5.66 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: 0.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 3.130 Check model and map are aligned: 0.210 Set scattering table: 0.140 Process input model: 42.250 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.490 ------------------------------------------------------------------------------- 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 : 1.936 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 outliers start: 16 outliers final: 4 residues processed: 628 average time/residue: 0.3367 time to fit residues: 289.5575 Evaluate side-chains 352 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 348 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1304 time to fit residues: 3.2794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 8.9990 chunk 133 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 71 optimal weight: 0.0870 chunk 137 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 102 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 overall best weight: 2.5762 ------------------------------------------------------------------------------- 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: 0.8444 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15648 Z= 0.305 Angle : 0.794 10.113 21132 Z= 0.399 Chirality : 0.053 0.265 2104 Planarity : 0.006 0.046 2728 Dihedral : 6.573 26.635 2004 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 3.46 % Allowed : 16.79 % Favored : 79.75 % 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: -3.83 (0.18), residues: 1752 helix: -2.86 (0.18), residues: 536 sheet: -2.36 (0.25), residues: 360 loop : -2.32 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 174 HIS 0.008 0.001 HIS L 43 PHE 0.020 0.003 PHE E 127 TYR 0.024 0.002 TYR B 29 ARG 0.004 0.001 ARG K 147 *********************** 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 432 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 376 time to evaluate : 1.861 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 outliers start: 56 outliers final: 24 residues processed: 404 average time/residue: 0.2766 time to fit residues: 162.5532 Evaluate side-chains 308 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 284 time to evaluate : 1.845 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1391 time to fit residues: 8.6720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 88 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 108 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 172 optimal weight: 2.9990 chunk 142 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 128 optimal weight: 2.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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 ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS D 249 HIS ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS G 249 HIS ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 HIS J 249 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 15648 Z= 0.301 Angle : 0.771 11.037 21132 Z= 0.380 Chirality : 0.052 0.281 2104 Planarity : 0.005 0.044 2728 Dihedral : 6.050 23.541 2004 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 3.70 % Allowed : 17.78 % 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: -3.45 (0.19), residues: 1752 helix: -2.42 (0.19), residues: 592 sheet: -1.82 (0.27), residues: 360 loop : -2.29 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 174 HIS 0.005 0.001 HIS L 43 PHE 0.022 0.002 PHE J 202 TYR 0.017 0.002 TYR A 308 ARG 0.003 0.001 ARG E 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 376 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 316 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 20 residues processed: 348 average time/residue: 0.2115 time to fit residues: 117.8005 Evaluate side-chains 300 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 280 time to evaluate : 1.789 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1405 time to fit residues: 7.6593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 0.1980 chunk 120 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 160 optimal weight: 6.9990 chunk 170 optimal weight: 2.9990 chunk 152 optimal weight: 0.3980 chunk 45 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS B 134 GLN C 3 ASN D 227 HIS E 134 GLN F 3 ASN G 227 HIS H 134 GLN I 3 ASN J 227 HIS K 134 GLN L 3 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15648 Z= 0.175 Angle : 0.672 8.608 21132 Z= 0.327 Chirality : 0.048 0.227 2104 Planarity : 0.004 0.047 2728 Dihedral : 5.534 20.672 2004 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 1.98 % Allowed : 19.51 % 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: -3.12 (0.19), residues: 1752 helix: -2.13 (0.19), residues: 588 sheet: -1.54 (0.27), residues: 356 loop : -2.18 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 277 HIS 0.005 0.001 HIS J 249 PHE 0.018 0.002 PHE A 202 TYR 0.021 0.001 TYR B 29 ARG 0.004 0.000 ARG E 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 376 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 344 time to evaluate : 1.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 8 residues processed: 372 average time/residue: 0.2162 time to fit residues: 128.1698 Evaluate side-chains 280 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 272 time to evaluate : 1.873 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1339 time to fit residues: 4.4258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 96 optimal weight: 10.0000 chunk 2 optimal weight: 0.0170 chunk 126 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 152 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 overall best weight: 5.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 HIS B 14 ASN ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN ** D 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 14 ASN ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 158 GLN ** G 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS H 14 ASN ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 158 GLN ** J 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 HIS K 14 ASN ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.064 15648 Z= 0.548 Angle : 0.852 7.663 21132 Z= 0.442 Chirality : 0.055 0.288 2104 Planarity : 0.006 0.043 2728 Dihedral : 6.226 24.565 2004 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.56 % Favored : 87.44 % Rotamer: Outliers : 5.19 % Allowed : 20.62 % Favored : 74.20 % 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: -3.18 (0.19), residues: 1752 helix: -1.91 (0.20), residues: 596 sheet: -1.80 (0.27), residues: 356 loop : -2.32 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 277 HIS 0.012 0.002 HIS G 249 PHE 0.023 0.003 PHE K 44 TYR 0.015 0.002 TYR G 269 ARG 0.005 0.001 ARG K 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 360 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 276 time to evaluate : 1.806 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 outliers start: 84 outliers final: 56 residues processed: 332 average time/residue: 0.2466 time to fit residues: 124.9171 Evaluate side-chains 308 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 252 time to evaluate : 1.852 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.1400 time to fit residues: 16.9423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 153 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 170 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN D 227 HIS F 3 ASN F 158 GLN G 227 HIS I 3 ASN I 158 GLN J 227 HIS ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.4891 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= 0.212 Angle : 0.708 8.841 21132 Z= 0.345 Chirality : 0.050 0.224 2104 Planarity : 0.004 0.044 2728 Dihedral : 5.737 22.416 2004 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % Rotamer: Outliers : 0.86 % Allowed : 23.58 % Favored : 75.56 % 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: -2.84 (0.19), residues: 1752 helix: -1.59 (0.21), residues: 596 sheet: -1.53 (0.27), residues: 356 loop : -2.20 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP L 174 HIS 0.011 0.002 HIS D 249 PHE 0.012 0.002 PHE E 127 TYR 0.014 0.001 TYR L 40 ARG 0.004 0.000 ARG J 248 *********************** 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 312 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 298 time to evaluate : 1.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 312 average time/residue: 0.2115 time to fit residues: 105.6728 Evaluate side-chains 286 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 280 time to evaluate : 1.886 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1329 time to fit residues: 4.0590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 19 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 143 optimal weight: 9.9990 chunk 95 optimal weight: 0.7980 chunk 169 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS C 3 ASN ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS G 227 HIS J 227 HIS L 3 ASN ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15648 Z= 0.185 Angle : 0.706 11.258 21132 Z= 0.334 Chirality : 0.049 0.274 2104 Planarity : 0.004 0.046 2728 Dihedral : 5.361 21.134 2004 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 1.60 % Allowed : 25.43 % Favored : 72.96 % 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: -2.61 (0.19), residues: 1752 helix: -1.36 (0.21), residues: 588 sheet: -1.39 (0.27), residues: 356 loop : -2.10 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 277 HIS 0.006 0.001 HIS G 249 PHE 0.017 0.002 PHE A 202 TYR 0.012 0.001 TYR F 40 ARG 0.003 0.000 ARG B 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 336 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 310 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 328 average time/residue: 0.2140 time to fit residues: 113.5479 Evaluate side-chains 294 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 284 time to evaluate : 1.839 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1379 time to fit residues: 5.0807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 67 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 73 HIS ** C 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 63 ASN F 3 ASN F 73 HIS F 158 GLN G 227 HIS H 63 ASN I 3 ASN I 73 HIS I 158 GLN J 227 HIS K 63 ASN L 73 HIS ** L 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15648 Z= 0.323 Angle : 0.740 8.381 21132 Z= 0.363 Chirality : 0.051 0.298 2104 Planarity : 0.005 0.044 2728 Dihedral : 5.515 21.843 2004 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 2.65 % Allowed : 25.37 % Favored : 71.98 % 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: -2.49 (0.20), residues: 1752 helix: -1.20 (0.22), residues: 592 sheet: -1.38 (0.27), residues: 356 loop : -2.05 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 174 HIS 0.006 0.001 HIS G 249 PHE 0.014 0.002 PHE H 44 TYR 0.012 0.001 TYR C 40 ARG 0.003 0.000 ARG H 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 332 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 289 time to evaluate : 1.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 26 residues processed: 312 average time/residue: 0.2134 time to fit residues: 106.7801 Evaluate side-chains 298 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 272 time to evaluate : 1.787 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1428 time to fit residues: 9.2956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 162 optimal weight: 7.9990 chunk 148 optimal weight: 6.9990 chunk 158 optimal weight: 6.9990 chunk 95 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 142 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 chunk 157 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN C 73 HIS C 158 GLN D 227 HIS ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 HIS G 227 HIS I 73 HIS J 227 HIS ** K 104 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: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5263 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= 0.236 Angle : 0.728 12.687 21132 Z= 0.352 Chirality : 0.050 0.272 2104 Planarity : 0.004 0.045 2728 Dihedral : 5.423 22.945 2004 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 17.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.11 % Allowed : 25.93 % Favored : 72.96 % 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: -2.51 (0.19), residues: 1752 helix: -1.17 (0.22), residues: 592 sheet: -1.29 (0.27), residues: 356 loop : -2.17 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 174 HIS 0.015 0.001 HIS G 249 PHE 0.017 0.002 PHE A 202 TYR 0.012 0.001 TYR C 40 ARG 0.003 0.000 ARG B 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 338 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 320 time to evaluate : 1.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 10 residues processed: 330 average time/residue: 0.2094 time to fit residues: 111.0298 Evaluate side-chains 284 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 274 time to evaluate : 1.700 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1340 time to fit residues: 4.8238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 167 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 175 optimal weight: 0.9990 chunk 161 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 85 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 73 HIS D 227 HIS E 63 ASN E 133 GLN F 3 ASN F 73 HIS G 227 HIS H 63 ASN H 133 GLN I 3 ASN I 73 HIS J 227 HIS K 63 ASN ** L 73 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 15648 Z= 0.258 Angle : 0.753 11.987 21132 Z= 0.362 Chirality : 0.051 0.286 2104 Planarity : 0.004 0.045 2728 Dihedral : 5.360 24.898 2004 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.50 % Favored : 91.50 % Rotamer: Outliers : 0.68 % Allowed : 27.65 % Favored : 71.67 % 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: -2.47 (0.19), residues: 1752 helix: -1.21 (0.21), residues: 588 sheet: -1.23 (0.27), residues: 356 loop : -2.10 (0.21), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP J 277 HIS 0.013 0.001 HIS G 249 PHE 0.011 0.002 PHE H 127 TYR 0.013 0.001 TYR F 40 ARG 0.003 0.000 ARG K 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 301 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 290 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 2 residues processed: 299 average time/residue: 0.2145 time to fit residues: 103.3691 Evaluate side-chains 281 residues out of total 1620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 279 time to evaluate : 1.884 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1405 time to fit residues: 3.0520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 148 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 143 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 HIS D 227 HIS E 63 ASN F 73 HIS G 227 HIS H 63 ASN I 73 HIS J 227 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 73 HIS L 158 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.121021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.092869 restraints weight = 32407.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.095408 restraints weight = 21508.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.097025 restraints weight = 16883.265| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 15648 Z= 0.372 Angle : 0.790 11.664 21132 Z= 0.391 Chirality : 0.053 0.308 2104 Planarity : 0.005 0.043 2728 Dihedral : 5.600 24.965 2004 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 19.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 0.62 % Allowed : 27.90 % Favored : 71.48 % 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: -2.43 (0.19), residues: 1752 helix: -1.15 (0.21), residues: 588 sheet: -1.18 (0.27), residues: 348 loop : -2.11 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 277 HIS 0.014 0.002 HIS J 249 PHE 0.016 0.002 PHE E 44 TYR 0.017 0.002 TYR C 40 ARG 0.004 0.000 ARG K 33 =============================================================================== Job complete usr+sys time: 3139.05 seconds wall clock time: 58 minutes 1.74 seconds (3481.74 seconds total)