Starting phenix.real_space_refine on Wed Mar 4 15:49:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nil_9380/03_2026/6nil_9380.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nil_9380/03_2026/6nil_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 { model { file = "/net/cci-nas-00/data/ceres_data/6nil_9380/03_2026/6nil_9380.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nil_9380/03_2026/6nil_9380.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nil_9380/03_2026/6nil_9380.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nil_9380/03_2026/6nil_9380.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15220 Number of models: 1 Model: "" Number of chains: 4 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: "A" 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 Restraints were copied for chains: D, G, J, E, H, K, F, I, L Time building chain proxies: 2.33, per 1000 atoms: 0.15 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 - 3.00 Amino acid : True - 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: 0.93 Conformation dependent library (CDL) restraints added in 658.3 milliseconds 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: 0.59 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: 2.20 Time building geometry restraints manager: 1.32 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: 0.00 - 1.97: 20228 1.97 - 3.94: 732 3.94 - 5.91: 124 5.91 - 7.88: 40 7.88 - 9.85: 8 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 3.040 nonbonded pdb=" O TRP A 277 " pdb=" OG1 THR A 303 " model vdw 2.396 3.040 nonbonded pdb=" O TRP G 277 " pdb=" OG1 THR G 303 " model vdw 2.396 3.040 nonbonded pdb=" O TRP J 277 " pdb=" OG1 THR J 303 " model vdw 2.396 3.040 nonbonded pdb=" O ILE C 107 " pdb=" N TYR C 111 " model vdw 2.459 3.120 ... (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 Time spend for trying shortcut: 0.06 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.820 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.030 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:1.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.840 ------------------------------------------------------------------------------- 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 : 0.010 0.423 15660 Z= 0.455 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG D 293 TYR 0.014 0.002 TYR L 44 PHE 0.009 0.001 PHE A 200 TRP 0.016 0.002 TRP L 174 HIS 0.006 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00531 (15648) covalent geometry : angle 0.95681 (21132) hydrogen bonds : bond 0.25006 ( 404) hydrogen bonds : angle 11.70200 ( 1224) metal coordination : bond 0.29858 ( 12) *********************** 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 to be fit. rotamer outliers: 16 poor density : 620 time to evaluate : 0.676 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: 0.8209 (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: 0.9001 (tp30) REVERT: A 319 ARG cc_start: 0.9153 (mtp180) cc_final: 0.8939 (mtp180) REVERT: A 331 MET cc_start: 0.8128 (ptm) cc_final: 0.7661 (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: 0.7023 (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: 0.7835 (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: 0.8329 (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: 0.8227 (mtp85) cc_final: 0.7802 (mtp180) REVERT: D 252 ARG cc_start: 0.9448 (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: 0.8998 (tp30) REVERT: D 319 ARG cc_start: 0.9153 (mtp180) cc_final: 0.8939 (mtp180) REVERT: D 331 MET cc_start: 0.8129 (ptm) cc_final: 0.7662 (ptm) REVERT: E 34 ASP cc_start: 0.7951 (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: 0.7027 (p) REVERT: E 117 GLN cc_start: 0.8965 (tt0) cc_final: 0.8605 (pt0) REVERT: E 127 PHE cc_start: 0.8533 (t80) cc_final: 0.7830 (t80) REVERT: F 1 MET cc_start: 0.6109 (tpt) cc_final: 0.5489 (ptt) REVERT: F 6 GLN cc_start: 0.8877 (tt0) cc_final: 0.8453 (tt0) REVERT: F 8 MET cc_start: 0.9058 (mtt) cc_final: 0.8819 (mpp) REVERT: F 14 ASP cc_start: 0.9215 (p0) cc_final: 0.8655 (p0) REVERT: F 79 TRP cc_start: 0.9083 (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: 0.9331 (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: 0.8998 (tp30) REVERT: G 319 ARG cc_start: 0.9153 (mtp180) cc_final: 0.8939 (mtp180) REVERT: G 331 MET cc_start: 0.8127 (ptm) cc_final: 0.7657 (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: 0.7028 (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: 0.7828 (t80) REVERT: I 1 MET cc_start: 0.6111 (tpt) cc_final: 0.5492 (ptt) REVERT: I 6 GLN cc_start: 0.8877 (tt0) cc_final: 0.8453 (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: 0.8330 (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: 0.8438 (mm) cc_final: 0.8211 (pt) REVERT: J 248 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7802 (mtp180) REVERT: J 252 ARG cc_start: 0.9447 (ttp80) cc_final: 0.9231 (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: 0.9000 (tp30) REVERT: J 319 ARG cc_start: 0.9154 (mtp180) cc_final: 0.8941 (mtp180) REVERT: J 331 MET cc_start: 0.8129 (ptm) cc_final: 0.7661 (ptm) REVERT: K 34 ASP cc_start: 0.7953 (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: 0.9218 (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: 0.7025 (p) REVERT: K 117 GLN cc_start: 0.8964 (tt0) cc_final: 0.8605 (pt0) REVERT: K 127 PHE cc_start: 0.8535 (t80) cc_final: 0.7833 (t80) REVERT: L 1 MET cc_start: 0.6108 (tpt) cc_final: 0.5488 (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: 0.8520 (mt0) REVERT: L 107 ILE cc_start: 0.9384 (OUTLIER) cc_final: 0.9106 (mp) REVERT: L 109 LEU cc_start: 0.8704 (mt) cc_final: 0.8471 (tp) outliers start: 16 outliers final: 4 residues processed: 628 average time/residue: 0.1472 time to fit residues: 128.4089 Evaluate side-chains 416 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 404 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.0470 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN D 227 HIS ** E 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN G 227 HIS ** H 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 227 HIS ** K 8 GLN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.124131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096181 restraints weight = 32880.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.098898 restraints weight = 20183.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.100707 restraints weight = 15127.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.101736 restraints weight = 12655.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.102532 restraints weight = 11384.844| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15660 Z= 0.168 Angle : 0.765 9.813 21132 Z= 0.385 Chirality : 0.053 0.292 2104 Planarity : 0.006 0.067 2728 Dihedral : 8.193 80.344 2032 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.31 % Favored : 92.69 % Rotamer: Outliers : 3.21 % Allowed : 14.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.88 (0.18), residues: 1752 helix: -2.93 (0.17), residues: 540 sheet: -2.29 (0.25), residues: 360 loop : -2.37 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 77 TYR 0.024 0.002 TYR B 29 PHE 0.020 0.002 PHE H 18 TRP 0.014 0.001 TRP C 174 HIS 0.008 0.001 HIS C 43 Details of bonding type rmsd covalent geometry : bond 0.00387 (15648) covalent geometry : angle 0.76492 (21132) hydrogen bonds : bond 0.03754 ( 404) hydrogen bonds : angle 6.94350 ( 1224) metal coordination : bond 0.00148 ( 12) *********************** 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 to be fit. rotamer outliers: 52 poor density : 432 time to evaluate : 0.609 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: A 252 ARG cc_start: 0.8807 (ttp80) cc_final: 0.8559 (ttp80) REVERT: A 346 ASN cc_start: 0.8262 (p0) cc_final: 0.7988 (p0) REVERT: B 8 GLN cc_start: 0.4492 (pp30) cc_final: 0.4258 (pp30) REVERT: B 117 GLN cc_start: 0.8170 (tt0) cc_final: 0.7945 (pt0) REVERT: B 133 GLN cc_start: 0.7146 (mp10) cc_final: 0.6835 (mp10) REVERT: C 1 MET cc_start: 0.6974 (tpt) cc_final: 0.5337 (ptt) REVERT: C 91 LYS cc_start: 0.7824 (tptt) cc_final: 0.7573 (mtmt) REVERT: C 105 GLN cc_start: 0.7830 (mt0) cc_final: 0.7438 (mp10) REVERT: D 252 ARG cc_start: 0.8815 (ttp80) cc_final: 0.8560 (ttp80) REVERT: D 346 ASN cc_start: 0.8268 (p0) cc_final: 0.8001 (p0) REVERT: E 8 GLN cc_start: 0.4495 (pp30) cc_final: 0.4257 (pp30) REVERT: E 117 GLN cc_start: 0.8187 (tt0) cc_final: 0.7949 (pt0) REVERT: E 133 GLN cc_start: 0.7142 (mp10) cc_final: 0.6833 (mp10) REVERT: F 1 MET cc_start: 0.6982 (tpt) cc_final: 0.5346 (ptt) REVERT: F 91 LYS cc_start: 0.7824 (tptt) cc_final: 0.7575 (mtmt) REVERT: F 105 GLN cc_start: 0.7827 (mt0) cc_final: 0.7439 (mp10) REVERT: G 252 ARG cc_start: 0.8814 (ttp80) cc_final: 0.8556 (ttp80) REVERT: G 346 ASN cc_start: 0.8257 (p0) cc_final: 0.7983 (p0) REVERT: H 8 GLN cc_start: 0.4490 (pp30) cc_final: 0.4250 (pp30) REVERT: H 117 GLN cc_start: 0.8181 (tt0) cc_final: 0.7949 (pt0) REVERT: H 133 GLN cc_start: 0.7144 (mp10) cc_final: 0.6831 (mp10) REVERT: I 1 MET cc_start: 0.6977 (tpt) cc_final: 0.5344 (ptt) REVERT: I 91 LYS cc_start: 0.7816 (tptt) cc_final: 0.7563 (mtmt) REVERT: I 105 GLN cc_start: 0.7830 (mt0) cc_final: 0.7439 (mp10) REVERT: J 252 ARG cc_start: 0.8816 (ttp80) cc_final: 0.8556 (ttp80) REVERT: J 346 ASN cc_start: 0.8259 (p0) cc_final: 0.7982 (p0) REVERT: K 8 GLN cc_start: 0.4492 (pp30) cc_final: 0.4266 (pp30) REVERT: K 117 GLN cc_start: 0.8177 (tt0) cc_final: 0.7946 (pt0) REVERT: K 133 GLN cc_start: 0.7147 (mp10) cc_final: 0.6836 (mp10) REVERT: L 1 MET cc_start: 0.6981 (tpt) cc_final: 0.5345 (ptt) REVERT: L 91 LYS cc_start: 0.7824 (tptt) cc_final: 0.7577 (mtmt) REVERT: L 105 GLN cc_start: 0.7825 (mt0) cc_final: 0.7439 (mp10) outliers start: 52 outliers final: 24 residues processed: 468 average time/residue: 0.1269 time to fit residues: 86.0211 Evaluate side-chains 348 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 324 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 ILE Chi-restraints excluded: chain A residue 358 ASP 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 59 LEU Chi-restraints excluded: chain D residue 199 ILE Chi-restraints excluded: chain D residue 358 ASP 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 59 LEU Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 358 ASP 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 59 LEU Chi-restraints excluded: chain J residue 199 ILE Chi-restraints excluded: chain J residue 358 ASP 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 59 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 97 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 169 optimal weight: 0.9980 chunk 124 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 84 optimal weight: 0.5980 chunk 8 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 77 optimal weight: 0.0370 chunk 142 optimal weight: 4.9990 overall best weight: 0.8460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS B 37 HIS ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN D 227 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN G 227 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 227 HIS K 37 HIS ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.124723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.097475 restraints weight = 33597.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.100360 restraints weight = 20437.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102259 restraints weight = 15140.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.103458 restraints weight = 12564.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.104001 restraints weight = 11178.963| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15660 Z= 0.124 Angle : 0.727 12.358 21132 Z= 0.355 Chirality : 0.051 0.274 2104 Planarity : 0.005 0.046 2728 Dihedral : 5.873 21.206 2004 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 3.21 % Allowed : 16.54 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.60 (0.18), residues: 1752 helix: -2.58 (0.18), residues: 588 sheet: -2.19 (0.25), residues: 384 loop : -2.16 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 77 TYR 0.012 0.001 TYR L 40 PHE 0.024 0.002 PHE E 127 TRP 0.016 0.001 TRP F 5 HIS 0.006 0.001 HIS L 43 Details of bonding type rmsd covalent geometry : bond 0.00281 (15648) covalent geometry : angle 0.72656 (21132) hydrogen bonds : bond 0.03033 ( 404) hydrogen bonds : angle 6.34235 ( 1224) metal coordination : bond 0.00329 ( 12) *********************** 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 412 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 360 time to evaluate : 0.505 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 202 PHE cc_start: 0.7257 (t80) cc_final: 0.7018 (t80) REVERT: A 346 ASN cc_start: 0.8227 (p0) cc_final: 0.7977 (p0) REVERT: B 84 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6765 (pm20) REVERT: B 117 GLN cc_start: 0.8116 (tt0) cc_final: 0.7897 (pt0) REVERT: B 133 GLN cc_start: 0.7117 (mp10) cc_final: 0.6868 (mp10) REVERT: C 1 MET cc_start: 0.6614 (tpt) cc_final: 0.5431 (ptt) REVERT: C 91 LYS cc_start: 0.7729 (tptt) cc_final: 0.7523 (mtmt) REVERT: D 346 ASN cc_start: 0.8232 (p0) cc_final: 0.7987 (p0) REVERT: E 84 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: E 117 GLN cc_start: 0.8128 (tt0) cc_final: 0.7903 (pt0) REVERT: E 133 GLN cc_start: 0.7116 (mp10) cc_final: 0.6871 (mp10) REVERT: F 1 MET cc_start: 0.6616 (tpt) cc_final: 0.5435 (ptt) REVERT: F 91 LYS cc_start: 0.7731 (tptt) cc_final: 0.7528 (mtmt) REVERT: G 202 PHE cc_start: 0.7273 (t80) cc_final: 0.7036 (t80) REVERT: G 346 ASN cc_start: 0.8228 (p0) cc_final: 0.7976 (p0) REVERT: H 84 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6760 (pm20) REVERT: H 117 GLN cc_start: 0.8126 (tt0) cc_final: 0.7901 (pt0) REVERT: H 133 GLN cc_start: 0.7117 (mp10) cc_final: 0.6869 (mp10) REVERT: I 1 MET cc_start: 0.6612 (tpt) cc_final: 0.5428 (ptt) REVERT: I 91 LYS cc_start: 0.7727 (tptt) cc_final: 0.7524 (mtmt) REVERT: J 202 PHE cc_start: 0.7260 (t80) cc_final: 0.7023 (t80) REVERT: J 346 ASN cc_start: 0.8230 (p0) cc_final: 0.7981 (p0) REVERT: K 84 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6771 (pm20) REVERT: K 117 GLN cc_start: 0.8129 (tt0) cc_final: 0.7898 (pt0) REVERT: K 133 GLN cc_start: 0.7122 (mp10) cc_final: 0.6871 (mp10) REVERT: L 1 MET cc_start: 0.6617 (tpt) cc_final: 0.5435 (ptt) REVERT: L 91 LYS cc_start: 0.7727 (tptt) cc_final: 0.7521 (mtmt) outliers start: 52 outliers final: 28 residues processed: 392 average time/residue: 0.1067 time to fit residues: 64.2033 Evaluate side-chains 332 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 300 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 VAL 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 78 ASP Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 106 VAL 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 78 ASP Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 VAL 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 78 ASP Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 106 VAL 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 78 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 142 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 80 optimal weight: 0.2980 chunk 18 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 131 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 119 optimal weight: 0.8980 chunk 86 optimal weight: 0.0010 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 GLN C 3 ASN D 227 HIS E 37 HIS ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 134 GLN F 3 ASN G 227 HIS H 37 HIS ** H 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 134 GLN I 3 ASN J 227 HIS ** K 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 GLN L 3 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.125088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097038 restraints weight = 33602.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.099887 restraints weight = 20705.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.101706 restraints weight = 15511.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102940 restraints weight = 12978.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.103490 restraints weight = 11614.114| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 15660 Z= 0.118 Angle : 0.688 12.144 21132 Z= 0.334 Chirality : 0.049 0.235 2104 Planarity : 0.004 0.047 2728 Dihedral : 5.510 19.677 2004 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.53 % Favored : 92.47 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.23 (0.19), residues: 1752 helix: -2.22 (0.19), residues: 600 sheet: -1.87 (0.25), residues: 384 loop : -2.05 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 33 TYR 0.007 0.001 TYR J 359 PHE 0.018 0.002 PHE J 202 TRP 0.010 0.001 TRP I 5 HIS 0.005 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00269 (15648) covalent geometry : angle 0.68795 (21132) hydrogen bonds : bond 0.02799 ( 404) hydrogen bonds : angle 5.94461 ( 1224) metal coordination : bond 0.00162 ( 12) *********************** 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 380 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 312 time to evaluate : 0.435 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: A 346 ASN cc_start: 0.8256 (p0) cc_final: 0.8003 (p0) REVERT: B 84 GLU cc_start: 0.7138 (OUTLIER) cc_final: 0.6793 (pm20) REVERT: B 117 GLN cc_start: 0.8110 (tt0) cc_final: 0.7808 (pt0) REVERT: C 1 MET cc_start: 0.6681 (tpt) cc_final: 0.5451 (ptt) REVERT: D 202 PHE cc_start: 0.7365 (t80) cc_final: 0.7163 (t80) REVERT: D 346 ASN cc_start: 0.8260 (p0) cc_final: 0.8010 (p0) REVERT: E 84 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6787 (pm20) REVERT: E 117 GLN cc_start: 0.8098 (tt0) cc_final: 0.7806 (pt0) REVERT: F 1 MET cc_start: 0.6686 (tpt) cc_final: 0.5459 (ptt) REVERT: G 346 ASN cc_start: 0.8273 (p0) cc_final: 0.8018 (p0) REVERT: H 84 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6789 (pm20) REVERT: H 117 GLN cc_start: 0.8097 (tt0) cc_final: 0.7804 (pt0) REVERT: I 1 MET cc_start: 0.6677 (tpt) cc_final: 0.5451 (ptt) REVERT: J 346 ASN cc_start: 0.8253 (p0) cc_final: 0.8001 (p0) REVERT: K 84 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.6796 (pm20) REVERT: K 117 GLN cc_start: 0.8118 (tt0) cc_final: 0.7812 (pt0) REVERT: L 1 MET cc_start: 0.6679 (tpt) cc_final: 0.5451 (ptt) outliers start: 68 outliers final: 24 residues processed: 364 average time/residue: 0.1010 time to fit residues: 57.2938 Evaluate side-chains 316 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 288 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS 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 B residue 106 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 198 HIS 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 E residue 106 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain G residue 198 HIS 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 H residue 106 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain J residue 198 HIS 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 K residue 106 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 59 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 24 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 129 optimal weight: 0.8980 chunk 157 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 138 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 HIS ** K 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.125081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.097981 restraints weight = 33223.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100843 restraints weight = 20276.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.102672 restraints weight = 14998.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.103876 restraints weight = 12475.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.104643 restraints weight = 11099.303| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15660 Z= 0.121 Angle : 0.700 12.389 21132 Z= 0.336 Chirality : 0.050 0.250 2104 Planarity : 0.004 0.046 2728 Dihedral : 5.303 19.498 2004 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 4.20 % Allowed : 18.02 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.89 (0.19), residues: 1752 helix: -1.99 (0.20), residues: 604 sheet: -1.33 (0.26), residues: 360 loop : -2.02 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 33 TYR 0.006 0.001 TYR L 40 PHE 0.015 0.001 PHE B 17 TRP 0.009 0.001 TRP L 174 HIS 0.004 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00283 (15648) covalent geometry : angle 0.70014 (21132) hydrogen bonds : bond 0.02719 ( 404) hydrogen bonds : angle 5.71690 ( 1224) metal coordination : bond 0.00170 ( 12) *********************** 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 384 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 316 time to evaluate : 0.581 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: A 346 ASN cc_start: 0.8189 (p0) cc_final: 0.7926 (p0) REVERT: B 54 GLU cc_start: 0.8306 (pm20) cc_final: 0.8069 (pm20) REVERT: B 84 GLU cc_start: 0.7266 (OUTLIER) cc_final: 0.6867 (pm20) REVERT: B 117 GLN cc_start: 0.8097 (tt0) cc_final: 0.7895 (pt0) REVERT: C 1 MET cc_start: 0.6773 (tpt) cc_final: 0.5406 (ptt) REVERT: C 12 GLN cc_start: 0.8600 (pm20) cc_final: 0.7989 (pm20) REVERT: C 37 ASP cc_start: 0.7551 (p0) cc_final: 0.7329 (p0) REVERT: D 346 ASN cc_start: 0.8206 (p0) cc_final: 0.7945 (p0) REVERT: E 54 GLU cc_start: 0.8309 (pm20) cc_final: 0.8075 (pm20) REVERT: E 84 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: F 1 MET cc_start: 0.6774 (tpt) cc_final: 0.5404 (ptt) REVERT: F 12 GLN cc_start: 0.8609 (pm20) cc_final: 0.8000 (pm20) REVERT: F 37 ASP cc_start: 0.7572 (p0) cc_final: 0.7346 (p0) REVERT: G 346 ASN cc_start: 0.8213 (p0) cc_final: 0.7943 (p0) REVERT: H 54 GLU cc_start: 0.8300 (pm20) cc_final: 0.8062 (pm20) REVERT: H 84 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6865 (pm20) REVERT: I 1 MET cc_start: 0.6772 (tpt) cc_final: 0.5402 (ptt) REVERT: I 12 GLN cc_start: 0.8603 (pm20) cc_final: 0.7991 (pm20) REVERT: I 37 ASP cc_start: 0.7556 (p0) cc_final: 0.7331 (p0) REVERT: J 346 ASN cc_start: 0.8211 (p0) cc_final: 0.7943 (p0) REVERT: K 54 GLU cc_start: 0.8302 (pm20) cc_final: 0.8066 (pm20) REVERT: K 84 GLU cc_start: 0.7262 (OUTLIER) cc_final: 0.6870 (pm20) REVERT: L 1 MET cc_start: 0.6767 (tpt) cc_final: 0.5404 (ptt) REVERT: L 12 GLN cc_start: 0.8604 (pm20) cc_final: 0.7992 (pm20) REVERT: L 37 ASP cc_start: 0.7553 (p0) cc_final: 0.7326 (p0) outliers start: 68 outliers final: 32 residues processed: 368 average time/residue: 0.0922 time to fit residues: 54.5634 Evaluate side-chains 320 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 284 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS 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 B residue 106 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 78 ASP Chi-restraints excluded: chain D residue 198 HIS 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 E residue 106 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 78 ASP Chi-restraints excluded: chain G residue 198 HIS 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 H residue 106 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 36 LYS Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain I residue 78 ASP Chi-restraints excluded: chain J residue 198 HIS 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 K residue 106 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 59 LEU Chi-restraints excluded: chain L residue 78 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 132 optimal weight: 0.0670 chunk 82 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 ASN D 227 HIS ** E 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 3 ASN G 227 HIS ** H 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 3 ASN J 227 HIS ** K 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.122710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.095985 restraints weight = 32736.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.098751 restraints weight = 20172.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.100544 restraints weight = 15079.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.101696 restraints weight = 12604.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.102408 restraints weight = 11263.482| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.4657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15660 Z= 0.145 Angle : 0.708 12.356 21132 Z= 0.340 Chirality : 0.050 0.246 2104 Planarity : 0.004 0.045 2728 Dihedral : 5.211 20.306 2004 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.76 % Favored : 92.24 % Rotamer: Outliers : 3.46 % Allowed : 18.89 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.67 (0.19), residues: 1752 helix: -1.83 (0.20), residues: 596 sheet: -1.15 (0.26), residues: 360 loop : -1.91 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.016 0.001 TYR A 359 PHE 0.028 0.002 PHE J 202 TRP 0.012 0.001 TRP I 11 HIS 0.004 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00342 (15648) covalent geometry : angle 0.70760 (21132) hydrogen bonds : bond 0.02838 ( 404) hydrogen bonds : angle 5.58624 ( 1224) metal coordination : bond 0.00214 ( 12) *********************** 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 356 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 300 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 ASN cc_start: 0.8281 (p0) cc_final: 0.7999 (p0) REVERT: B 54 GLU cc_start: 0.8400 (pm20) cc_final: 0.7986 (pm20) REVERT: B 130 GLU cc_start: 0.8441 (mp0) cc_final: 0.8004 (pp20) REVERT: C 1 MET cc_start: 0.6825 (tpt) cc_final: 0.5419 (ptt) REVERT: C 37 ASP cc_start: 0.7642 (p0) cc_final: 0.7408 (p0) REVERT: D 346 ASN cc_start: 0.8292 (p0) cc_final: 0.8016 (p0) REVERT: E 54 GLU cc_start: 0.8400 (pm20) cc_final: 0.7988 (pm20) REVERT: E 130 GLU cc_start: 0.8439 (mp0) cc_final: 0.8003 (pp20) REVERT: F 1 MET cc_start: 0.6827 (tpt) cc_final: 0.5415 (ptt) REVERT: F 37 ASP cc_start: 0.7640 (p0) cc_final: 0.7405 (p0) REVERT: G 346 ASN cc_start: 0.8292 (p0) cc_final: 0.8007 (p0) REVERT: H 54 GLU cc_start: 0.8395 (pm20) cc_final: 0.7985 (pm20) REVERT: H 84 GLU cc_start: 0.7428 (OUTLIER) cc_final: 0.7072 (pm20) REVERT: H 130 GLU cc_start: 0.8448 (mp0) cc_final: 0.8001 (pp20) REVERT: I 1 MET cc_start: 0.6822 (tpt) cc_final: 0.5410 (ptt) REVERT: I 37 ASP cc_start: 0.7650 (p0) cc_final: 0.7412 (p0) REVERT: J 346 ASN cc_start: 0.8279 (p0) cc_final: 0.8003 (p0) REVERT: K 54 GLU cc_start: 0.8397 (pm20) cc_final: 0.7983 (pm20) REVERT: K 130 GLU cc_start: 0.8455 (mp0) cc_final: 0.8008 (pp20) REVERT: L 1 MET cc_start: 0.6820 (tpt) cc_final: 0.5414 (ptt) REVERT: L 37 ASP cc_start: 0.7644 (p0) cc_final: 0.7411 (p0) outliers start: 56 outliers final: 43 residues processed: 336 average time/residue: 0.0985 time to fit residues: 52.6600 Evaluate side-chains 336 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 292 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 313 ASP Chi-restraints excluded: chain A residue 358 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 B residue 106 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 313 ASP Chi-restraints excluded: chain D residue 358 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 E residue 106 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 313 ASP Chi-restraints excluded: chain G residue 358 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 H residue 106 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 36 LYS Chi-restraints excluded: chain I residue 59 LEU Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 313 ASP Chi-restraints excluded: chain J residue 358 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 K residue 106 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 36 LYS Chi-restraints excluded: chain L residue 59 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 160 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 161 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 120 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN ** B 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 HIS E 63 ASN ** E 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 227 HIS H 63 ASN ** H 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 227 HIS ** K 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN ** K 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.124180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.097442 restraints weight = 32614.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100267 restraints weight = 20024.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.102131 restraints weight = 14890.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.103271 restraints weight = 12402.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.104052 restraints weight = 11078.315| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15660 Z= 0.126 Angle : 0.676 10.289 21132 Z= 0.327 Chirality : 0.049 0.248 2104 Planarity : 0.004 0.044 2728 Dihedral : 5.119 19.736 2004 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.72 % Allowed : 20.37 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.49 (0.19), residues: 1752 helix: -1.67 (0.21), residues: 596 sheet: -0.95 (0.27), residues: 360 loop : -1.87 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 33 TYR 0.015 0.001 TYR D 359 PHE 0.015 0.001 PHE K 17 TRP 0.008 0.001 TRP D 277 HIS 0.004 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00300 (15648) covalent geometry : angle 0.67574 (21132) hydrogen bonds : bond 0.02904 ( 404) hydrogen bonds : angle 5.45005 ( 1224) metal coordination : bond 0.00195 ( 12) *********************** 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 352 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 308 time to evaluate : 0.578 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: B 54 GLU cc_start: 0.8383 (pm20) cc_final: 0.8030 (pm20) REVERT: B 84 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7059 (pm20) REVERT: B 130 GLU cc_start: 0.8319 (mp0) cc_final: 0.7965 (pp20) REVERT: C 1 MET cc_start: 0.6717 (tpt) cc_final: 0.5459 (ptt) REVERT: C 37 ASP cc_start: 0.7695 (p0) cc_final: 0.7396 (p0) REVERT: E 54 GLU cc_start: 0.8386 (pm20) cc_final: 0.8034 (pm20) REVERT: E 84 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7062 (pm20) REVERT: E 130 GLU cc_start: 0.8319 (mp0) cc_final: 0.7968 (pp20) REVERT: F 1 MET cc_start: 0.6721 (tpt) cc_final: 0.5461 (ptt) REVERT: F 37 ASP cc_start: 0.7711 (p0) cc_final: 0.7413 (p0) REVERT: H 54 GLU cc_start: 0.8386 (pm20) cc_final: 0.8033 (pm20) REVERT: H 84 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7057 (pm20) REVERT: H 130 GLU cc_start: 0.8322 (mp0) cc_final: 0.7972 (pp20) REVERT: I 1 MET cc_start: 0.6713 (tpt) cc_final: 0.5449 (ptt) REVERT: I 37 ASP cc_start: 0.7708 (p0) cc_final: 0.7408 (p0) REVERT: K 54 GLU cc_start: 0.8375 (pm20) cc_final: 0.8025 (pm20) REVERT: K 84 GLU cc_start: 0.7413 (OUTLIER) cc_final: 0.7066 (pm20) REVERT: K 130 GLU cc_start: 0.8329 (mp0) cc_final: 0.7972 (pp20) REVERT: L 1 MET cc_start: 0.6713 (tpt) cc_final: 0.5458 (ptt) REVERT: L 37 ASP cc_start: 0.7705 (p0) cc_final: 0.7407 (p0) outliers start: 44 outliers final: 24 residues processed: 336 average time/residue: 0.0843 time to fit residues: 46.6774 Evaluate side-chains 311 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 283 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 63 ASN Chi-restraints excluded: chain B residue 84 GLU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 ASP Chi-restraints excluded: chain E residue 63 ASN Chi-restraints excluded: chain E residue 84 GLU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 358 ASP Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 84 GLU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 358 ASP Chi-restraints excluded: chain K residue 63 ASN Chi-restraints excluded: chain K residue 84 GLU Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 80 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 F 73 HIS G 227 HIS H 63 ASN I 73 HIS J 227 HIS ** K 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN L 73 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.121709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.094738 restraints weight = 32605.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.097483 restraints weight = 20145.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.099270 restraints weight = 15083.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.100418 restraints weight = 12644.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100997 restraints weight = 11286.836| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 15660 Z= 0.177 Angle : 0.768 13.990 21132 Z= 0.361 Chirality : 0.053 0.303 2104 Planarity : 0.004 0.041 2728 Dihedral : 5.212 20.247 2004 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 3.70 % Allowed : 21.60 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.52 (0.19), residues: 1752 helix: -1.58 (0.20), residues: 604 sheet: -0.94 (0.27), residues: 352 loop : -1.99 (0.20), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 148 TYR 0.014 0.001 TYR A 359 PHE 0.036 0.002 PHE G 202 TRP 0.013 0.001 TRP C 11 HIS 0.004 0.001 HIS F 43 Details of bonding type rmsd covalent geometry : bond 0.00421 (15648) covalent geometry : angle 0.76767 (21132) hydrogen bonds : bond 0.02933 ( 404) hydrogen bonds : angle 5.58344 ( 1224) metal coordination : bond 0.00306 ( 12) *********************** 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 340 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 280 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 GLU cc_start: 0.8416 (pm20) cc_final: 0.8046 (pm20) REVERT: B 130 GLU cc_start: 0.8489 (mp0) cc_final: 0.8022 (pp20) REVERT: C 1 MET cc_start: 0.6675 (tpt) cc_final: 0.5416 (ptt) REVERT: E 29 TYR cc_start: 0.8644 (t80) cc_final: 0.8350 (t80) REVERT: E 54 GLU cc_start: 0.8416 (pm20) cc_final: 0.8069 (pm20) REVERT: E 130 GLU cc_start: 0.8487 (mp0) cc_final: 0.8024 (pp20) REVERT: F 1 MET cc_start: 0.6678 (tpt) cc_final: 0.5419 (ptt) REVERT: H 29 TYR cc_start: 0.8644 (t80) cc_final: 0.8352 (t80) REVERT: H 54 GLU cc_start: 0.8411 (pm20) cc_final: 0.8066 (pm20) REVERT: H 130 GLU cc_start: 0.8493 (mp0) cc_final: 0.8027 (pp20) REVERT: I 1 MET cc_start: 0.6679 (tpt) cc_final: 0.5418 (ptt) REVERT: K 29 TYR cc_start: 0.8635 (t80) cc_final: 0.8344 (t80) REVERT: K 54 GLU cc_start: 0.8416 (pm20) cc_final: 0.8053 (pm20) REVERT: K 130 GLU cc_start: 0.8495 (mp0) cc_final: 0.8024 (pp20) REVERT: L 1 MET cc_start: 0.6673 (tpt) cc_final: 0.5414 (ptt) outliers start: 60 outliers final: 40 residues processed: 321 average time/residue: 0.0868 time to fit residues: 45.4869 Evaluate side-chains 320 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 280 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 358 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 B residue 106 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 358 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 E residue 106 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 36 LYS Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 357 LEU Chi-restraints excluded: chain G residue 358 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 H residue 106 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 36 LYS Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 357 LEU Chi-restraints excluded: chain J residue 358 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 K residue 106 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 36 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 8 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 175 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** B 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN D 227 HIS E 63 ASN G 227 HIS H 63 ASN J 227 HIS ** K 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.121103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.093821 restraints weight = 32470.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.096576 restraints weight = 20253.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.098353 restraints weight = 15220.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.099520 restraints weight = 12785.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.100156 restraints weight = 11414.912| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15660 Z= 0.189 Angle : 0.771 11.853 21132 Z= 0.364 Chirality : 0.054 0.292 2104 Planarity : 0.004 0.041 2728 Dihedral : 5.253 20.320 2004 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 3.46 % Allowed : 21.23 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.53 (0.19), residues: 1752 helix: -1.55 (0.20), residues: 604 sheet: -1.13 (0.27), residues: 364 loop : -1.96 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 148 TYR 0.014 0.001 TYR D 359 PHE 0.015 0.002 PHE K 44 TRP 0.011 0.001 TRP D 277 HIS 0.005 0.001 HIS L 73 Details of bonding type rmsd covalent geometry : bond 0.00446 (15648) covalent geometry : angle 0.77055 (21132) hydrogen bonds : bond 0.02985 ( 404) hydrogen bonds : angle 5.64877 ( 1224) metal coordination : bond 0.00308 ( 12) *********************** 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 345 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 289 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 347 ASP cc_start: 0.8404 (m-30) cc_final: 0.8111 (m-30) REVERT: B 54 GLU cc_start: 0.8467 (pm20) cc_final: 0.8076 (pm20) REVERT: C 1 MET cc_start: 0.6720 (tpt) cc_final: 0.5388 (ptt) REVERT: D 347 ASP cc_start: 0.8399 (m-30) cc_final: 0.8104 (m-30) REVERT: E 54 GLU cc_start: 0.8482 (pm20) cc_final: 0.8086 (pm20) REVERT: F 1 MET cc_start: 0.6728 (tpt) cc_final: 0.5391 (ptt) REVERT: G 347 ASP cc_start: 0.8394 (m-30) cc_final: 0.8099 (m-30) REVERT: H 54 GLU cc_start: 0.8474 (pm20) cc_final: 0.8080 (pm20) REVERT: I 1 MET cc_start: 0.6723 (tpt) cc_final: 0.5386 (ptt) REVERT: J 347 ASP cc_start: 0.8415 (m-30) cc_final: 0.8120 (m-30) REVERT: K 54 GLU cc_start: 0.8468 (pm20) cc_final: 0.8081 (pm20) REVERT: L 1 MET cc_start: 0.6724 (tpt) cc_final: 0.5384 (ptt) outliers start: 56 outliers final: 40 residues processed: 329 average time/residue: 0.0860 time to fit residues: 46.5098 Evaluate side-chains 325 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 285 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 357 LEU 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 102 ILE Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain C residue 73 HIS Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 357 LEU 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 102 ILE Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 73 HIS Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 357 LEU 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 102 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 106 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain I residue 73 HIS Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 357 LEU 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 102 ILE Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 106 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 73 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 89 optimal weight: 2.9990 chunk 140 optimal weight: 0.0470 chunk 40 optimal weight: 1.9990 chunk 143 optimal weight: 4.9990 chunk 129 optimal weight: 0.0670 chunk 170 optimal weight: 6.9990 chunk 139 optimal weight: 0.2980 chunk 90 optimal weight: 8.9990 chunk 93 optimal weight: 0.0470 chunk 22 optimal weight: 8.9990 chunk 162 optimal weight: 2.9990 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 HIS ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 63 ASN D 227 HIS ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN G 227 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN J 227 HIS ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.125088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.097820 restraints weight = 32846.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.100771 restraints weight = 20026.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.102687 restraints weight = 14836.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103929 restraints weight = 12315.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104631 restraints weight = 10937.468| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15660 Z= 0.117 Angle : 0.771 16.577 21132 Z= 0.350 Chirality : 0.052 0.288 2104 Planarity : 0.004 0.045 2728 Dihedral : 5.040 19.541 2004 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 2.22 % Allowed : 22.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.19), residues: 1752 helix: -1.49 (0.21), residues: 596 sheet: -0.90 (0.27), residues: 368 loop : -1.96 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.014 0.001 TYR D 359 PHE 0.020 0.001 PHE D 202 TRP 0.012 0.001 TRP L 11 HIS 0.006 0.001 HIS C 73 Details of bonding type rmsd covalent geometry : bond 0.00275 (15648) covalent geometry : angle 0.77055 (21132) hydrogen bonds : bond 0.02854 ( 404) hydrogen bonds : angle 5.39146 ( 1224) metal coordination : bond 0.00157 ( 12) ********************** 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 351 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 315 time to evaluate : 0.559 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: B 54 GLU cc_start: 0.8307 (pm20) cc_final: 0.8016 (pm20) REVERT: B 84 GLU cc_start: 0.7491 (OUTLIER) cc_final: 0.7097 (pm20) REVERT: B 130 GLU cc_start: 0.8461 (mp0) cc_final: 0.8083 (pp20) REVERT: C 1 MET cc_start: 0.6998 (tpt) cc_final: 0.5518 (ptt) REVERT: E 54 GLU cc_start: 0.8345 (pm20) cc_final: 0.8063 (pm20) REVERT: E 84 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7121 (pm20) REVERT: E 130 GLU cc_start: 0.8455 (mp0) cc_final: 0.8081 (pp20) REVERT: F 1 MET cc_start: 0.6999 (tpt) cc_final: 0.5516 (ptt) REVERT: H 54 GLU cc_start: 0.8346 (pm20) cc_final: 0.8061 (pm20) REVERT: H 84 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7118 (pm20) REVERT: H 130 GLU cc_start: 0.8459 (mp0) cc_final: 0.8085 (pp20) REVERT: I 1 MET cc_start: 0.6996 (tpt) cc_final: 0.5512 (ptt) REVERT: K 54 GLU cc_start: 0.8340 (pm20) cc_final: 0.8058 (pm20) REVERT: K 84 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7125 (pm20) REVERT: K 130 GLU cc_start: 0.8464 (mp0) cc_final: 0.8083 (pp20) REVERT: L 1 MET cc_start: 0.6997 (tpt) cc_final: 0.5513 (ptt) outliers start: 36 outliers final: 28 residues processed: 339 average time/residue: 0.0845 time to fit residues: 47.5719 Evaluate side-chains 309 residues out of total 1620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 277 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 HIS Chi-restraints excluded: chain A residue 357 LEU 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 B residue 106 VAL Chi-restraints excluded: chain C residue 20 THR Chi-restraints excluded: chain D residue 198 HIS Chi-restraints excluded: chain D residue 357 LEU 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 E residue 106 VAL Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain G residue 198 HIS Chi-restraints excluded: chain G residue 357 LEU 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 H residue 106 VAL Chi-restraints excluded: chain I residue 20 THR Chi-restraints excluded: chain J residue 198 HIS Chi-restraints excluded: chain J residue 357 LEU 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 K residue 106 VAL Chi-restraints excluded: chain L residue 20 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 99 optimal weight: 8.9990 chunk 164 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 151 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 139 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 D 227 HIS ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 ASN G 227 HIS ** H 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN J 227 HIS K 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.123533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096470 restraints weight = 32508.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.099286 restraints weight = 20158.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.101156 restraints weight = 15005.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.102301 restraints weight = 12487.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.103129 restraints weight = 11128.935| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15660 Z= 0.140 Angle : 0.765 14.275 21132 Z= 0.352 Chirality : 0.053 0.271 2104 Planarity : 0.004 0.045 2728 Dihedral : 4.994 19.577 2004 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 1.98 % Allowed : 23.40 % Favored : 74.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.23 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.19), residues: 1752 helix: -1.42 (0.21), residues: 600 sheet: -0.80 (0.27), residues: 368 loop : -2.00 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 33 TYR 0.014 0.001 TYR G 359 PHE 0.019 0.001 PHE A 202 TRP 0.008 0.001 TRP D 277 HIS 0.004 0.001 HIS I 73 Details of bonding type rmsd covalent geometry : bond 0.00338 (15648) covalent geometry : angle 0.76532 (21132) hydrogen bonds : bond 0.02811 ( 404) hydrogen bonds : angle 5.43976 ( 1224) metal coordination : bond 0.00196 ( 12) =============================================================================== Job complete usr+sys time: 2332.01 seconds wall clock time: 41 minutes 3.98 seconds (2463.98 seconds total)