Starting phenix.real_space_refine on Wed Feb 21 21:22:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9e_4481/02_2024/6q9e_4481_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9e_4481/02_2024/6q9e_4481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9e_4481/02_2024/6q9e_4481.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9e_4481/02_2024/6q9e_4481.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9e_4481/02_2024/6q9e_4481_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q9e_4481/02_2024/6q9e_4481_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.018 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: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 14 5.49 5 S 164 5.16 5 C 20484 2.51 5 N 5441 2.21 5 O 5884 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a1 PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a1 PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a2 ARG 240": "NH1" <-> "NH2" Residue "a2 PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a2 PHE 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b1 TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c1 PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d1 ARG 48": "NH1" <-> "NH2" Residue "d1 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q1 ARG 2": "NH1" <-> "NH2" Residue "h1 ARG 34": "NH1" <-> "NH2" Residue "a3 PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a4 ARG 240": "NH1" <-> "NH2" Residue "a4 PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b2 PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b2 TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b2 ARG 313": "NH1" <-> "NH2" Residue "c2 ARG 139": "NH1" <-> "NH2" Residue "d2 TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h2 PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31997 Number of models: 1 Model: "" Number of chains: 26 Chain: "a1" Number of atoms: 3409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3409 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 18, 'TRANS': 420} Chain breaks: 1 Chain: "a2" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3126 Classifications: {'peptide': 414} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 399} Chain breaks: 1 Chain: "b1" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3019 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 353} Chain: "c1" Number of atoms: 1909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1909 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 22, 'TRANS': 216} Chain: "f1" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1520 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "d1" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 886 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 96} Chain: "q1" Number of atoms: 618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 618 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 5, 'TRANS': 67} Chain: "h1" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "x1" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 164 Classifications: {'peptide': 33} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 32} Link IDs: {'TRANS': 32} Chain breaks: 1 Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 101 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 33} Unresolved non-hydrogen planarities: 33 Chain: "i1" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 459 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "a3" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3447 Classifications: {'peptide': 444} Link IDs: {'PTRANS': 18, 'TRANS': 425} Chain: "a4" Number of atoms: 3122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 413, 3122 Classifications: {'peptide': 413} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 398} Chain breaks: 1 Chain: "b2" Number of atoms: 3019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3019 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 353} Chain: "c2" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1903 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 22, 'TRANS': 215} Chain: "f2" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 183} Chain: "d2" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 888 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "q2" Number of atoms: 631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 631 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 6, 'TRANS': 68} Chain: "h2" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 532 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "x2" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 150 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 29} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'UNK:plan-1': 30} Unresolved non-hydrogen planarities: 30 Chain: "i2" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 473 Classifications: {'peptide': 57} Link IDs: {'TRANS': 56} Chain: "b1" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 260 Unusual residues: {'3PE': 1, 'CDL': 2, 'HEM': 2, 'U10': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 203 Unresolved non-hydrogen angles: 218 Unresolved non-hydrogen dihedrals: 188 Planarities with less than four sites: {'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-4': 1, 'U10:plan-5': 2, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 60 Chain: "c1" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 87 Planarities with less than four sites: {'3PE:plan-1': 1, '3PE:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "f1" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "b2" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 189 Unusual residues: {'3PE': 1, 'CDL': 1, 'HEM': 2, 'U10': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 103 Planarities with less than four sites: {'U10:plan-8': 1, 'U10:plan-9': 1, 'U10:plan-4': 1, 'U10:plan-5': 1, 'U10:plan-6': 1, 'U10:plan-7': 1, 'U10:plan-10': 1, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 31 Chain: "c2" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 91 Unusual residues: {'CDL': 1, 'HEC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Chain: "f2" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'3PE': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12558 SG CYSf1 139 40.810 64.146 134.722 1.00154.41 S ATOM 12694 SG CYSf1 158 42.886 67.388 135.383 1.00144.15 S ATOM 28222 SG CYSf2 139 105.183 57.153 121.799 1.00143.28 S ATOM 28358 SG CYSf2 158 103.339 53.723 121.745 1.00139.12 S Time building chain proxies: 15.72, per 1000 atoms: 0.49 Number of scatterers: 31997 At special positions: 0 Unit cell: (134.4, 151.2, 176.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 164 16.00 P 14 15.00 O 5884 8.00 N 5441 7.00 C 20484 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYSf1 144 " - pdb=" SG CYSf1 160 " distance=2.03 Simple disulfide: pdb=" SG CYSh1 24 " - pdb=" SG CYSh1 68 " distance=2.03 Simple disulfide: pdb=" SG CYSh1 40 " - pdb=" SG CYSh1 54 " distance=2.03 Simple disulfide: pdb=" SG CYSf2 144 " - pdb=" SG CYSf2 160 " distance=2.04 Simple disulfide: pdb=" SG CYSh2 24 " - pdb=" SG CYSh2 68 " distance=2.02 Simple disulfide: pdb=" SG CYSh2 40 " - pdb=" SG CYSh2 54 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.45 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FESf1 501 " pdb="FE1 FESf1 501 " - pdb=" SG CYSf1 139 " pdb="FE1 FESf1 501 " - pdb=" SG CYSf1 158 " pdb="FE2 FESf1 501 " - pdb=" ND1 HISf1 161 " pdb="FE2 FESf1 501 " - pdb=" ND1 HISf1 141 " pdb=" FESf2 202 " pdb="FE1 FESf2 202 " - pdb=" SG CYSf2 158 " pdb="FE1 FESf2 202 " - pdb=" SG CYSf2 139 " pdb="FE2 FESf2 202 " - pdb=" ND1 HISf2 141 " pdb="FE2 FESf2 202 " - pdb=" ND1 HISf2 161 " Number of angles added : 6 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7474 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 13 sheets defined 49.5% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.08 Creating SS restraints... Processing helix chain 'a1' and resid 4 through 9 Processing helix chain 'a1' and resid 55 through 64 removed outlier: 5.604A pdb=" N PHEa1 64 " --> pdb=" O GLUa1 60 " (cutoff:3.500A) Processing helix chain 'a1' and resid 74 through 82 Processing helix chain 'a1' and resid 103 through 118 removed outlier: 3.598A pdb=" N LEUa1 106 " --> pdb=" O SERa1 103 " (cutoff:3.500A) Proline residue: a1 107 - end of helix removed outlier: 3.529A pdb=" N LEUa1 112 " --> pdb=" O ALAa1 109 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLNa1 118 " --> pdb=" O ASPa1 115 " (cutoff:3.500A) Processing helix chain 'a1' and resid 124 through 141 Processing helix chain 'a1' and resid 145 through 157 Processing helix chain 'a1' and resid 162 through 164 No H-bonds generated for 'chain 'a1' and resid 162 through 164' Processing helix chain 'a1' and resid 179 through 189 Processing helix chain 'a1' and resid 205 through 215 Processing helix chain 'a1' and resid 265 through 277 Processing helix chain 'a1' and resid 293 through 300 Processing helix chain 'a1' and resid 331 through 347 Processing helix chain 'a1' and resid 351 through 368 Processing helix chain 'a1' and resid 373 through 384 Processing helix chain 'a1' and resid 392 through 400 Processing helix chain 'a1' and resid 404 through 414 Processing helix chain 'a1' and resid 434 through 441 Processing helix chain 'a2' and resid 55 through 57 No H-bonds generated for 'chain 'a2' and resid 55 through 57' Processing helix chain 'a2' and resid 65 through 70 Processing helix chain 'a2' and resid 82 through 92 Processing helix chain 'a2' and resid 113 through 128 removed outlier: 4.206A pdb=" N VALa2 116 " --> pdb=" O ARGa2 113 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ASPa2 117 " --> pdb=" O ASPa2 114 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILEa2 118 " --> pdb=" O ASPa2 115 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEUa2 119 " --> pdb=" O VALa2 116 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THRa2 127 " --> pdb=" O LEUa2 124 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THRa2 128 " --> pdb=" O ASNa2 125 " (cutoff:3.500A) Processing helix chain 'a2' and resid 134 through 153 Processing helix chain 'a2' and resid 155 through 166 Processing helix chain 'a2' and resid 171 through 173 No H-bonds generated for 'chain 'a2' and resid 171 through 173' Processing helix chain 'a2' and resid 188 through 198 Processing helix chain 'a2' and resid 213 through 222 Processing helix chain 'a2' and resid 267 through 279 Processing helix chain 'a2' and resid 294 through 302 Processing helix chain 'a2' and resid 333 through 348 Processing helix chain 'a2' and resid 354 through 370 Processing helix chain 'a2' and resid 375 through 388 Processing helix chain 'a2' and resid 395 through 403 Processing helix chain 'a2' and resid 407 through 419 Processing helix chain 'b1' and resid 9 through 18 removed outlier: 3.963A pdb=" N ILEb1 13 " --> pdb=" O PROb1 9 " (cutoff:3.500A) Processing helix chain 'b1' and resid 29 through 54 removed outlier: 3.899A pdb=" N PHEb1 33 " --> pdb=" O TRPb1 30 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLYb1 34 " --> pdb=" O TRPb1 31 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEUb1 36 " --> pdb=" O PHEb1 33 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYSb1 40 " --> pdb=" O LEUb1 37 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THRb1 47 " --> pdb=" O GLNb1 44 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLYb1 48 " --> pdb=" O ILEb1 45 " (cutoff:3.500A) Processing helix chain 'b1' and resid 62 through 71 Processing helix chain 'b1' and resid 76 through 103 Processing helix chain 'b1' and resid 106 through 108 No H-bonds generated for 'chain 'b1' and resid 106 through 108' Processing helix chain 'b1' and resid 111 through 133 Processing helix chain 'b1' and resid 137 through 152 Processing helix chain 'b1' and resid 157 through 164 Processing helix chain 'b1' and resid 172 through 203 Proline residue: b1 186 - end of helix Processing helix chain 'b1' and resid 224 through 244 Processing helix chain 'b1' and resid 253 through 255 No H-bonds generated for 'chain 'b1' and resid 253 through 255' Processing helix chain 'b1' and resid 272 through 281 removed outlier: 3.553A pdb=" N LEUb1 275 " --> pdb=" O TRPb1 272 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N PHEb1 276 " --> pdb=" O TYRb1 273 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALAb1 277 " --> pdb=" O PHEb1 274 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILEb1 280 " --> pdb=" O ALAb1 277 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEUb1 281 " --> pdb=" O TYRb1 278 " (cutoff:3.500A) Processing helix chain 'b1' and resid 287 through 307 Proline residue: b1 305 - end of helix Processing helix chain 'b1' and resid 319 through 339 Processing helix chain 'b1' and resid 345 through 363 Processing helix chain 'b1' and resid 365 through 376 Processing helix chain 'c1' and resid 23 through 35 Processing helix chain 'c1' and resid 37 through 39 No H-bonds generated for 'chain 'c1' and resid 37 through 39' Processing helix chain 'c1' and resid 48 through 51 Processing helix chain 'c1' and resid 59 through 67 Processing helix chain 'c1' and resid 98 through 104 removed outlier: 3.754A pdb=" N ALAc1 104 " --> pdb=" O ALAc1 100 " (cutoff:3.500A) Processing helix chain 'c1' and resid 116 through 119 No H-bonds generated for 'chain 'c1' and resid 116 through 119' Processing helix chain 'c1' and resid 124 through 132 Processing helix chain 'c1' and resid 178 through 193 Processing helix chain 'c1' and resid 197 through 227 removed outlier: 4.026A pdb=" N LEUc1 215 " --> pdb=" O METc1 211 " (cutoff:3.500A) Proline residue: c1 216 - end of helix removed outlier: 3.871A pdb=" N TYRc1 219 " --> pdb=" O LEUc1 215 " (cutoff:3.500A) Processing helix chain 'f1' and resid 16 through 18 No H-bonds generated for 'chain 'f1' and resid 16 through 18' Processing helix chain 'f1' and resid 29 through 61 Processing helix chain 'f1' and resid 103 through 110 Processing helix chain 'f1' and resid 123 through 126 No H-bonds generated for 'chain 'f1' and resid 123 through 126' Processing helix chain 'd1' and resid 12 through 23 Processing helix chain 'd1' and resid 33 through 35 No H-bonds generated for 'chain 'd1' and resid 33 through 35' Processing helix chain 'd1' and resid 41 through 48 Processing helix chain 'd1' and resid 52 through 70 Processing helix chain 'd1' and resid 77 through 79 No H-bonds generated for 'chain 'd1' and resid 77 through 79' Processing helix chain 'd1' and resid 83 through 85 No H-bonds generated for 'chain 'd1' and resid 83 through 85' Processing helix chain 'd1' and resid 91 through 109 Processing helix chain 'q1' and resid 33 through 42 Processing helix chain 'q1' and resid 45 through 70 Proline residue: q1 50 - end of helix removed outlier: 3.933A pdb=" N VALq1 54 " --> pdb=" O PROq1 50 " (cutoff:3.500A) Processing helix chain 'h1' and resid 16 through 24 Processing helix chain 'h1' and resid 28 through 46 Processing helix chain 'h1' and resid 56 through 71 Processing helix chain 'i1' and resid 7 through 13 Processing helix chain 'i1' and resid 18 through 43 Processing helix chain 'i1' and resid 52 through 57 Processing helix chain 'a3' and resid 4 through 9 Processing helix chain 'a3' and resid 56 through 62 Processing helix chain 'a3' and resid 74 through 81 Processing helix chain 'a3' and resid 103 through 117 removed outlier: 3.688A pdb=" N LEUa3 106 " --> pdb=" O SERa3 103 " (cutoff:3.500A) Proline residue: a3 107 - end of helix Processing helix chain 'a3' and resid 124 through 143 removed outlier: 3.931A pdb=" N THRa3 143 " --> pdb=" O GLNa3 139 " (cutoff:3.500A) Processing helix chain 'a3' and resid 146 through 157 Processing helix chain 'a3' and resid 162 through 164 No H-bonds generated for 'chain 'a3' and resid 162 through 164' Processing helix chain 'a3' and resid 179 through 188 Processing helix chain 'a3' and resid 192 through 194 No H-bonds generated for 'chain 'a3' and resid 192 through 194' Processing helix chain 'a3' and resid 206 through 215 Processing helix chain 'a3' and resid 266 through 276 Processing helix chain 'a3' and resid 293 through 300 Processing helix chain 'a3' and resid 331 through 347 Processing helix chain 'a3' and resid 351 through 368 Processing helix chain 'a3' and resid 372 through 385 Processing helix chain 'a3' and resid 392 through 400 Processing helix chain 'a3' and resid 404 through 414 Processing helix chain 'a3' and resid 434 through 441 Processing helix chain 'a4' and resid 65 through 74 removed outlier: 4.349A pdb=" N SERa4 73 " --> pdb=" O LEUa4 69 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SERa4 74 " --> pdb=" O ARGa4 70 " (cutoff:3.500A) Processing helix chain 'a4' and resid 82 through 91 Processing helix chain 'a4' and resid 116 through 128 Processing helix chain 'a4' and resid 134 through 153 Processing helix chain 'a4' and resid 155 through 167 Processing helix chain 'a4' and resid 171 through 173 No H-bonds generated for 'chain 'a4' and resid 171 through 173' Processing helix chain 'a4' and resid 188 through 198 Processing helix chain 'a4' and resid 201 through 203 No H-bonds generated for 'chain 'a4' and resid 201 through 203' Processing helix chain 'a4' and resid 213 through 223 Processing helix chain 'a4' and resid 267 through 279 Processing helix chain 'a4' and resid 294 through 302 Processing helix chain 'a4' and resid 333 through 348 Processing helix chain 'a4' and resid 354 through 370 Processing helix chain 'a4' and resid 375 through 388 Processing helix chain 'a4' and resid 395 through 403 Processing helix chain 'a4' and resid 407 through 419 Processing helix chain 'b2' and resid 4 through 6 No H-bonds generated for 'chain 'b2' and resid 4 through 6' Processing helix chain 'b2' and resid 9 through 18 removed outlier: 3.920A pdb=" N ILEb2 13 " --> pdb=" O PROb2 9 " (cutoff:3.500A) Processing helix chain 'b2' and resid 29 through 53 removed outlier: 3.885A pdb=" N PHEb2 33 " --> pdb=" O TRPb2 30 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLYb2 34 " --> pdb=" O TRPb2 31 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEUb2 36 " --> pdb=" O PHEb2 33 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILEb2 39 " --> pdb=" O LEUb2 36 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYSb2 40 " --> pdb=" O LEUb2 37 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THRb2 47 " --> pdb=" O GLNb2 44 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLYb2 48 " --> pdb=" O ILEb2 45 " (cutoff:3.500A) Processing helix chain 'b2' and resid 62 through 71 Processing helix chain 'b2' and resid 76 through 103 Processing helix chain 'b2' and resid 106 through 108 No H-bonds generated for 'chain 'b2' and resid 106 through 108' Processing helix chain 'b2' and resid 110 through 133 Processing helix chain 'b2' and resid 137 through 152 Processing helix chain 'b2' and resid 157 through 164 Processing helix chain 'b2' and resid 172 through 203 Proline residue: b2 186 - end of helix Processing helix chain 'b2' and resid 224 through 244 Processing helix chain 'b2' and resid 253 through 256 removed outlier: 3.715A pdb=" N TYRb2 256 " --> pdb=" O PROb2 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'b2' and resid 253 through 256' Processing helix chain 'b2' and resid 272 through 283 removed outlier: 5.366A pdb=" N PHEb2 276 " --> pdb=" O TYRb2 273 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYRb2 278 " --> pdb=" O LEUb2 275 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALAb2 279 " --> pdb=" O PHEb2 276 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARGb2 282 " --> pdb=" O ALAb2 279 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SERb2 283 " --> pdb=" O ILEb2 280 " (cutoff:3.500A) Processing helix chain 'b2' and resid 287 through 302 Processing helix chain 'b2' and resid 305 through 307 No H-bonds generated for 'chain 'b2' and resid 305 through 307' Processing helix chain 'b2' and resid 319 through 339 Processing helix chain 'b2' and resid 345 through 363 Processing helix chain 'b2' and resid 365 through 376 Processing helix chain 'c2' and resid 23 through 35 Processing helix chain 'c2' and resid 48 through 52 removed outlier: 3.501A pdb=" N VALc2 52 " --> pdb=" O ARGc2 49 " (cutoff:3.500A) Processing helix chain 'c2' and resid 58 through 66 Processing helix chain 'c2' and resid 98 through 104 Processing helix chain 'c2' and resid 117 through 119 No H-bonds generated for 'chain 'c2' and resid 117 through 119' Processing helix chain 'c2' and resid 124 through 132 Processing helix chain 'c2' and resid 179 through 193 Processing helix chain 'c2' and resid 197 through 213 Processing helix chain 'c2' and resid 215 through 225 Processing helix chain 'c2' and resid 227 through 230 No H-bonds generated for 'chain 'c2' and resid 227 through 230' Processing helix chain 'f2' and resid 30 through 61 Processing helix chain 'f2' and resid 103 through 111 Processing helix chain 'f2' and resid 123 through 126 No H-bonds generated for 'chain 'f2' and resid 123 through 126' Processing helix chain 'd2' and resid 10 through 24 Processing helix chain 'd2' and resid 26 through 29 Processing helix chain 'd2' and resid 33 through 35 No H-bonds generated for 'chain 'd2' and resid 33 through 35' Processing helix chain 'd2' and resid 41 through 48 Processing helix chain 'd2' and resid 52 through 70 Processing helix chain 'd2' and resid 77 through 79 No H-bonds generated for 'chain 'd2' and resid 77 through 79' Processing helix chain 'd2' and resid 89 through 108 Proline residue: d2 92 - end of helix removed outlier: 3.529A pdb=" N LYSd2 102 " --> pdb=" O ARGd2 99 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLUd2 106 " --> pdb=" O GLUd2 103 " (cutoff:3.500A) Processing helix chain 'q2' and resid 33 through 42 Processing helix chain 'q2' and resid 45 through 70 Proline residue: q2 50 - end of helix removed outlier: 4.084A pdb=" N VALq2 54 " --> pdb=" O PROq2 50 " (cutoff:3.500A) Processing helix chain 'h2' and resid 16 through 24 Processing helix chain 'h2' and resid 29 through 45 Processing helix chain 'h2' and resid 56 through 70 Processing helix chain 'h2' and resid 74 through 76 No H-bonds generated for 'chain 'h2' and resid 74 through 76' Processing helix chain 'i2' and resid 7 through 13 Processing helix chain 'i2' and resid 18 through 47 removed outlier: 3.865A pdb=" N ASNi2 47 " --> pdb=" O TYRi2 43 " (cutoff:3.500A) Processing helix chain 'i2' and resid 52 through 57 Processing sheet with id= A, first strand: chain 'a1' and resid 15 through 19 Processing sheet with id= B, first strand: chain 'a1' and resid 239 through 244 Processing sheet with id= C, first strand: chain 'a2' and resid 25 through 29 Processing sheet with id= D, first strand: chain 'a2' and resid 243 through 247 removed outlier: 6.685A pdb=" N METa2 424 " --> pdb=" O ILEa2 244 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLUa2 246 " --> pdb=" O METa2 424 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALAa2 426 " --> pdb=" O GLUa2 246 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'b1' and resid 22 through 24 Processing sheet with id= F, first strand: chain 'f1' and resid 74 through 77 Processing sheet with id= G, first strand: chain 'f1' and resid 85 through 91 Processing sheet with id= H, first strand: chain 'a3' and resid 14 through 19 Processing sheet with id= I, first strand: chain 'a3' and resid 240 through 244 removed outlier: 6.375A pdb=" N VALa3 422 " --> pdb=" O ILEa3 241 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N HISa3 243 " --> pdb=" O VALa3 422 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLYa3 424 " --> pdb=" O HISa3 243 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ASPa3 327 " --> pdb=" O CYSa3 304 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N CYSa3 304 " --> pdb=" O ASPa3 327 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'a4' and resid 25 through 29 Processing sheet with id= K, first strand: chain 'a4' and resid 242 through 247 Processing sheet with id= L, first strand: chain 'f2' and resid 74 through 77 Processing sheet with id= M, first strand: chain 'f2' and resid 86 through 88 1545 hydrogen bonds defined for protein. 4293 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: 10.37 Time building geometry restraints manager: 13.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 12238 1.38 - 1.58: 20233 1.58 - 1.79: 89 1.79 - 1.99: 201 1.99 - 2.19: 24 Bond restraints: 32785 Sorted by residual: bond pdb=" C2D HECc2 501 " pdb=" C3D HECc2 501 " ideal model delta sigma weight residual 1.544 1.316 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C2D HECc1 501 " pdb=" C3D HECc1 501 " ideal model delta sigma weight residual 1.544 1.317 0.227 2.00e-02 2.50e+03 1.29e+02 bond pdb=" CAC HECc2 501 " pdb=" CBC HECc2 501 " ideal model delta sigma weight residual 1.544 1.362 0.182 2.00e-02 2.50e+03 8.27e+01 bond pdb=" CAC HECc1 501 " pdb=" CBC HECc1 501 " ideal model delta sigma weight residual 1.544 1.363 0.181 2.00e-02 2.50e+03 8.22e+01 bond pdb=" C4 U10b1 406 " pdb=" O4 U10b1 406 " ideal model delta sigma weight residual 1.230 1.410 -0.180 2.00e-02 2.50e+03 8.14e+01 ... (remaining 32780 not shown) Histogram of bond angle deviations from ideal: 87.22 - 105.47: 839 105.47 - 123.72: 42394 123.72 - 141.97: 1293 141.97 - 160.22: 0 160.22 - 178.47: 12 Bond angle restraints: 44538 Sorted by residual: angle pdb=" S1 FESf1 501 " pdb="FE2 FESf1 501 " pdb=" S2 FESf1 501 " ideal model delta sigma weight residual 104.33 90.01 14.32 1.14e+00 7.69e-01 1.58e+02 angle pdb="FE1 FESf1 501 " pdb=" S2 FESf1 501 " pdb="FE2 FESf1 501 " ideal model delta sigma weight residual 75.66 89.80 -14.14 1.14e+00 7.69e-01 1.54e+02 angle pdb=" S1 FESf2 202 " pdb="FE2 FESf2 202 " pdb=" S2 FESf2 202 " ideal model delta sigma weight residual 104.33 90.27 14.06 1.14e+00 7.69e-01 1.52e+02 angle pdb="FE1 FESf1 501 " pdb=" S1 FESf1 501 " pdb="FE2 FESf1 501 " ideal model delta sigma weight residual 75.66 90.17 -14.51 1.20e+00 6.94e-01 1.46e+02 angle pdb="FE1 FESf2 202 " pdb=" S2 FESf2 202 " pdb="FE2 FESf2 202 " ideal model delta sigma weight residual 75.66 89.44 -13.78 1.14e+00 7.69e-01 1.46e+02 ... (remaining 44533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 19218 35.88 - 71.76: 263 71.76 - 107.65: 43 107.65 - 143.53: 2 143.53 - 179.41: 3 Dihedral angle restraints: 19529 sinusoidal: 7931 harmonic: 11598 Sorted by residual: dihedral pdb=" CA ARGq1 11 " pdb=" C ARGq1 11 " pdb=" N HISq1 12 " pdb=" CA HISq1 12 " ideal model delta harmonic sigma weight residual -180.00 -115.42 -64.58 0 5.00e+00 4.00e-02 1.67e+02 dihedral pdb=" CB CYSh1 24 " pdb=" SG CYSh1 24 " pdb=" SG CYSh1 68 " pdb=" CB CYSh1 68 " ideal model delta sinusoidal sigma weight residual 93.00 179.42 -86.42 1 1.00e+01 1.00e-02 9.00e+01 dihedral pdb=" CB CYSh2 24 " pdb=" SG CYSh2 24 " pdb=" SG CYSh2 68 " pdb=" CB CYSh2 68 " ideal model delta sinusoidal sigma weight residual -86.00 -168.77 82.77 1 1.00e+01 1.00e-02 8.39e+01 ... (remaining 19526 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 4558 0.111 - 0.221: 269 0.221 - 0.332: 6 0.332 - 0.443: 2 0.443 - 0.553: 2 Chirality restraints: 4837 Sorted by residual: chirality pdb=" CB4 CDLc2 502 " pdb=" CB3 CDLc2 502 " pdb=" CB6 CDLc2 502 " pdb=" OB6 CDLc2 502 " both_signs ideal model delta sigma weight residual False -2.57 -2.02 -0.55 2.00e-01 2.50e+01 7.66e+00 chirality pdb=" CB ILEq2 34 " pdb=" CA ILEq2 34 " pdb=" CG1 ILEq2 34 " pdb=" CG2 ILEq2 34 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA4 CDLb2 404 " pdb=" CA3 CDLb2 404 " pdb=" CA6 CDLb2 404 " pdb=" OA6 CDLb2 404 " both_signs ideal model delta sigma weight residual False -2.57 -2.15 -0.42 2.00e-01 2.50e+01 4.43e+00 ... (remaining 4834 not shown) Planarity restraints: 5675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PROq1 50 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PROq1 51 " -0.187 5.00e-02 4.00e+02 pdb=" CA PROq1 51 " 0.055 5.00e-02 4.00e+02 pdb=" CD PROq1 51 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHEb1 183 " -0.030 2.00e-02 2.50e+03 3.18e-02 1.77e+01 pdb=" CG PHEb1 183 " 0.071 2.00e-02 2.50e+03 pdb=" CD1 PHEb1 183 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 PHEb1 183 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHEb1 183 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHEb1 183 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHEb1 183 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PROq2 50 " -0.065 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PROq2 51 " 0.169 5.00e-02 4.00e+02 pdb=" CA PROq2 51 " -0.049 5.00e-02 4.00e+02 pdb=" CD PROq2 51 " -0.055 5.00e-02 4.00e+02 ... (remaining 5672 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 218 2.56 - 3.15: 24749 3.15 - 3.73: 49294 3.73 - 4.32: 67084 4.32 - 4.90: 111426 Nonbonded interactions: 252771 Sorted by model distance: nonbonded pdb=" NE2 HISb1 182 " pdb="FE HEMb1 401 " model vdw 1.981 3.080 nonbonded pdb=" NE2 HISc1 41 " pdb="FE HECc1 501 " model vdw 1.990 3.080 nonbonded pdb=" NE2 HISb2 182 " pdb="FE HEMb2 401 " model vdw 2.000 3.080 nonbonded pdb=" NE2 HISb2 97 " pdb="FE HEMb2 402 " model vdw 2.052 3.080 nonbonded pdb=" NE2 HISb1 97 " pdb="FE HEMb1 402 " model vdw 2.098 3.080 ... (remaining 252766 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'a1' and resid 2 through 445) selection = (chain 'a3' and (resid 2 through 222 or resid 229 through 445)) } ncs_group { reference = (chain 'a2' and (resid 20 through 227 or resid 235 through 439)) selection = chain 'a4' } ncs_group { reference = (chain 'b1' and (resid 2 through 379 or resid 401 through 402 or (resid 403 and \ (name N or name C1 or name C11 or name C12 or name C2 or name C21 or name C22 or \ name C23 or name C24 or name C25 or name C26 or name C27 or name C28 or name C2 \ 9 or name C2A or name C2B or name C2C or name C2D or name C2E or name C2F or nam \ e C2G or name C2H or name C3 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name O11 or name O12 or name O13 or name O14 or name O21 or name O22 \ or name O31 or name O32 or name P )) or (resid 404 and (name CB2 or name OB2 or \ name CB3 or name OB3 or name C1 or name C11 or name C12 or name C31 or name C32 \ or name C33 or name C51 or name C52 or name C71 or name C72 or name CA2 or name \ CA3 or name CA4 or name CA5 or name CA6 or name CA7 or name CB4 or name CB5 or \ name CB6 or name CB7 or name O1 or name OA2 or name OA3 or name OA4 or name OA5 \ or name OA6 or name OA7 or name OA8 or name OA9 or name OB4 or name OB5 or name \ OB6 or name OB7 or name OB8 or name OB9 or name PA1 or name PB2)))) selection = (chain 'b2' and (resid 2 through 379 or resid 401 through 404)) } ncs_group { reference = (chain 'c1' and (resid 2 through 239 or resid 501)) selection = (chain 'c2' and (resid 2 through 239 or resid 501)) } ncs_group { reference = (chain 'd1' and resid 11 through 109) selection = (chain 'd2' and resid 11 through 109) } ncs_group { reference = (chain 'f1' and resid 2 through 196) selection = (chain 'f2' and resid 2 through 196) } ncs_group { reference = chain 'h1' selection = chain 'h2' } ncs_group { reference = chain 'i1' selection = (chain 'i2' and resid 5 through 59) } ncs_group { reference = (chain 'q1' and resid 2 through 73) selection = (chain 'q2' and resid 2 through 73) } ncs_group { reference = (chain 'x1' and resid 8 through 38) selection = (chain 'x2' and (resid 1 or (resid 2 and (name N or name CA or name C or name O \ )) or resid 3 through 48)) } 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.320 Check model and map are aligned: 0.440 Set scattering table: 0.260 Process input model: 84.790 Find NCS groups from input model: 2.310 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 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 : 0.009 0.228 32785 Z= 0.613 Angle : 1.075 15.525 44538 Z= 0.580 Chirality : 0.059 0.553 4837 Planarity : 0.009 0.108 5675 Dihedral : 12.975 179.409 12037 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.47 % Favored : 91.50 % Rotamer: Outliers : 0.42 % Allowed : 3.60 % Favored : 95.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.51 (0.11), residues: 3883 helix: -1.87 (0.09), residues: 2017 sheet: -1.42 (0.25), residues: 377 loop : -3.10 (0.14), residues: 1489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRPa3 443 HIS 0.020 0.002 HISi2 57 PHE 0.071 0.003 PHEb1 183 TYR 0.033 0.003 TYRc1 164 ARG 0.010 0.001 ARGa2 245 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1132 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1118 time to evaluate : 3.595 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: a1 57 TYR cc_start: 0.7779 (t80) cc_final: 0.6451 (t80) REVERT: a1 130 GLU cc_start: 0.8074 (mm-30) cc_final: 0.7596 (tp30) REVERT: a1 327 ASP cc_start: 0.8442 (t70) cc_final: 0.7826 (p0) REVERT: a1 329 MET cc_start: 0.8543 (mmm) cc_final: 0.8032 (tpt) REVERT: a1 346 CYS cc_start: 0.7797 (m) cc_final: 0.7124 (t) REVERT: a2 206 LEU cc_start: 0.8869 (tp) cc_final: 0.8441 (tt) REVERT: a2 351 ASN cc_start: 0.7356 (m110) cc_final: 0.6778 (t0) REVERT: a2 356 ASP cc_start: 0.7594 (m-30) cc_final: 0.7226 (t0) REVERT: b1 35 SER cc_start: 0.8897 (p) cc_final: 0.7995 (m) REVERT: b1 73 VAL cc_start: 0.9690 (t) cc_final: 0.9479 (m) REVERT: b1 240 MET cc_start: 0.8412 (mmp) cc_final: 0.7988 (mmm) REVERT: b1 243 VAL cc_start: 0.9078 (m) cc_final: 0.8799 (m) REVERT: b1 269 LYS cc_start: 0.8250 (pttt) cc_final: 0.7902 (ptpt) REVERT: b1 275 LEU cc_start: 0.8392 (mt) cc_final: 0.7655 (mt) REVERT: b1 292 LEU cc_start: 0.8409 (tp) cc_final: 0.8207 (tt) REVERT: b1 304 MET cc_start: 0.8564 (mmm) cc_final: 0.8291 (mmm) REVERT: b1 312 GLN cc_start: 0.8676 (mp10) cc_final: 0.8290 (mm-40) REVERT: c1 75 ASN cc_start: 0.8447 (t0) cc_final: 0.8202 (t0) REVERT: c1 106 ASN cc_start: 0.6599 (t0) cc_final: 0.6006 (t0) REVERT: c1 163 ILE cc_start: 0.7127 (OUTLIER) cc_final: 0.6612 (mm) REVERT: c1 187 THR cc_start: 0.9264 (m) cc_final: 0.9020 (p) REVERT: c1 207 MET cc_start: 0.7946 (ttm) cc_final: 0.7396 (tmm) REVERT: c1 211 MET cc_start: 0.7514 (mmt) cc_final: 0.6801 (tmm) REVERT: f1 2 HIS cc_start: 0.8325 (p-80) cc_final: 0.7648 (p90) REVERT: f1 3 THR cc_start: 0.8978 (p) cc_final: 0.8629 (t) REVERT: f1 43 THR cc_start: 0.8399 (m) cc_final: 0.8176 (p) REVERT: f1 104 LYS cc_start: 0.8157 (mmmt) cc_final: 0.7621 (pttt) REVERT: f1 135 LEU cc_start: 0.5916 (mt) cc_final: 0.5606 (mt) REVERT: f1 136 ILE cc_start: 0.8210 (mm) cc_final: 0.7766 (mt) REVERT: d1 18 LYS cc_start: 0.8387 (tttt) cc_final: 0.8093 (ptpt) REVERT: d1 22 ASN cc_start: 0.8610 (t0) cc_final: 0.8378 (m110) REVERT: d1 42 ASP cc_start: 0.8233 (m-30) cc_final: 0.7899 (m-30) REVERT: d1 47 ILE cc_start: 0.9358 (mm) cc_final: 0.9084 (tp) REVERT: d1 66 LEU cc_start: 0.9002 (mt) cc_final: 0.8742 (mm) REVERT: d1 74 ILE cc_start: 0.8763 (mt) cc_final: 0.8385 (pt) REVERT: q1 3 GLN cc_start: 0.8634 (pm20) cc_final: 0.8432 (pm20) REVERT: q1 47 ARG cc_start: 0.8583 (mtt180) cc_final: 0.7106 (mmt180) REVERT: h1 20 VAL cc_start: 0.8593 (t) cc_final: 0.7622 (p) REVERT: h1 37 LEU cc_start: 0.8924 (tm) cc_final: 0.8607 (tt) REVERT: h1 43 ARG cc_start: 0.6892 (ttm170) cc_final: 0.6445 (mmm-85) REVERT: a3 53 ASN cc_start: 0.7864 (t160) cc_final: 0.7553 (t0) REVERT: a3 82 MET cc_start: 0.7447 (mtt) cc_final: 0.6966 (mtt) REVERT: a3 223 TYR cc_start: 0.5352 (t80) cc_final: 0.5145 (p90) REVERT: a3 234 CYS cc_start: 0.7575 (m) cc_final: 0.7246 (m) REVERT: a3 307 PHE cc_start: 0.8239 (p90) cc_final: 0.7431 (p90) REVERT: a3 329 MET cc_start: 0.8812 (mmm) cc_final: 0.8559 (mmm) REVERT: a3 369 LEU cc_start: 0.8669 (mt) cc_final: 0.8313 (tt) REVERT: a3 411 CYS cc_start: 0.8548 (m) cc_final: 0.8296 (m) REVERT: a3 439 SER cc_start: 0.8103 (t) cc_final: 0.7614 (p) REVERT: a4 68 LEU cc_start: 0.9455 (tp) cc_final: 0.9214 (tp) REVERT: a4 207 ILE cc_start: 0.9342 (mm) cc_final: 0.8964 (mm) REVERT: a4 308 ASP cc_start: 0.8577 (t0) cc_final: 0.7606 (m-30) REVERT: a4 402 ILE cc_start: 0.8645 (mt) cc_final: 0.8278 (mt) REVERT: b2 27 ILE cc_start: 0.8130 (OUTLIER) cc_final: 0.7462 (mt) REVERT: b2 35 SER cc_start: 0.8811 (p) cc_final: 0.8060 (p) REVERT: b2 43 LEU cc_start: 0.8846 (tt) cc_final: 0.8204 (mt) REVERT: b2 200 LEU cc_start: 0.9414 (tp) cc_final: 0.9140 (tt) REVERT: b2 207 ASN cc_start: 0.8164 (p0) cc_final: 0.7934 (p0) REVERT: b2 252 ASP cc_start: 0.8183 (m-30) cc_final: 0.7905 (m-30) REVERT: b2 263 ASN cc_start: 0.8224 (t0) cc_final: 0.7982 (t0) REVERT: b2 278 TYR cc_start: 0.8454 (t80) cc_final: 0.7837 (t80) REVERT: b2 280 ILE cc_start: 0.8939 (mt) cc_final: 0.8731 (mm) REVERT: b2 320 ILE cc_start: 0.8368 (mt) cc_final: 0.8135 (tp) REVERT: c2 6 HIS cc_start: 0.8022 (t-90) cc_final: 0.7504 (m-70) REVERT: c2 76 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7801 (tp30) REVERT: c2 229 LEU cc_start: 0.9314 (mt) cc_final: 0.9101 (mt) REVERT: f2 69 LEU cc_start: 0.8728 (mm) cc_final: 0.8487 (tp) REVERT: f2 71 MET cc_start: 0.6135 (mmt) cc_final: 0.5766 (mmt) REVERT: f2 181 GLU cc_start: 0.8346 (tt0) cc_final: 0.7915 (tp30) REVERT: d2 88 PHE cc_start: 0.8125 (m-80) cc_final: 0.7808 (m-80) REVERT: d2 90 LEU cc_start: 0.9289 (tp) cc_final: 0.8868 (tt) REVERT: q2 2 ARG cc_start: 0.7912 (mtp85) cc_final: 0.6829 (ptt180) REVERT: q2 24 ARG cc_start: 0.7771 (ptp-110) cc_final: 0.7090 (tpt170) REVERT: q2 41 THR cc_start: 0.9379 (m) cc_final: 0.9005 (p) REVERT: q2 42 ARG cc_start: 0.8087 (tmt170) cc_final: 0.5880 (mtp85) REVERT: h2 26 GLN cc_start: 0.7441 (tp40) cc_final: 0.6972 (pm20) REVERT: h2 51 GLU cc_start: 0.7511 (tm-30) cc_final: 0.7101 (pm20) REVERT: i2 17 THR cc_start: 0.8798 (m) cc_final: 0.8519 (t) REVERT: i2 35 PHE cc_start: 0.8947 (t80) cc_final: 0.8714 (t80) outliers start: 14 outliers final: 3 residues processed: 1127 average time/residue: 0.4742 time to fit residues: 817.2361 Evaluate side-chains 639 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 634 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain c1 residue 163 ILE Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain b2 residue 27 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 328 optimal weight: 0.6980 chunk 294 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 304 optimal weight: 5.9990 chunk 117 optimal weight: 0.6980 chunk 185 optimal weight: 1.9990 chunk 226 optimal weight: 0.6980 chunk 353 optimal weight: 4.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 29 GLN a1 53 ASN ** a1 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1 189 HIS a1 264 ASN ** a1 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a1 341 GLN a2 22 GLN a2 104 ASN a2 125 ASN a2 248 ASN a2 290 ASN a2 297 GLN a2 313 ASN ** a2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 85 ASN c1 50 HIS ** c1 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 197 HIS c1 224 HIS f1 53 ASN f1 100 HIS ** d1 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q1 73 ASN ** h1 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i1 45 HIS a3 18 GLN a3 21 ASN a3 53 ASN a3 61 HIS a3 69 ASN a3 173 ASN a3 189 HIS a3 341 GLN a3 363 ASN a4 156 GLN ** a4 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a4 222 GLN a4 248 ASN a4 290 ASN a4 313 ASN a4 385 GLN b2 8 HIS b2 137 GLN b2 148 ASN b2 312 GLN c2 23 HIS c2 50 HIS ** c2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 197 HIS f2 108 GLN q2 6 HIS q2 23 GLN ** q2 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i2 54 HIS Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 32785 Z= 0.246 Angle : 0.747 17.267 44538 Z= 0.366 Chirality : 0.044 0.229 4837 Planarity : 0.006 0.087 5675 Dihedral : 12.304 146.924 4742 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 3.63 % Allowed : 13.63 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.13), residues: 3883 helix: -0.25 (0.11), residues: 2014 sheet: -0.83 (0.26), residues: 363 loop : -2.66 (0.15), residues: 1506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRPa3 443 HIS 0.015 0.001 HISa1 252 PHE 0.023 0.002 PHEb2 183 TYR 0.022 0.001 TYRb1 131 ARG 0.009 0.001 ARGa1 381 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 693 time to evaluate : 3.904 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: a1 60 GLU cc_start: 0.8688 (tt0) cc_final: 0.8183 (tt0) REVERT: a1 130 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7649 (tp30) REVERT: a1 271 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8138 (tp-100) REVERT: a1 320 LEU cc_start: 0.9390 (tp) cc_final: 0.9177 (tp) REVERT: a1 329 MET cc_start: 0.8467 (mmm) cc_final: 0.8124 (tpt) REVERT: a1 343 MET cc_start: 0.9090 (mmm) cc_final: 0.8884 (mmm) REVERT: a2 133 ARG cc_start: 0.6972 (mtm110) cc_final: 0.6737 (mtm110) REVERT: a2 206 LEU cc_start: 0.8949 (tp) cc_final: 0.8600 (tt) REVERT: b1 73 VAL cc_start: 0.9765 (t) cc_final: 0.9454 (m) REVERT: b1 175 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8785 (tp) REVERT: b1 237 LEU cc_start: 0.8542 (pp) cc_final: 0.8270 (mt) REVERT: b1 240 MET cc_start: 0.8485 (mmp) cc_final: 0.8144 (mmm) REVERT: b1 243 VAL cc_start: 0.9100 (m) cc_final: 0.8778 (m) REVERT: b1 278 TYR cc_start: 0.8706 (t80) cc_final: 0.8487 (t80) REVERT: b1 292 LEU cc_start: 0.8235 (tp) cc_final: 0.8008 (tt) REVERT: b1 311 LYS cc_start: 0.8664 (mmtm) cc_final: 0.8422 (mmtp) REVERT: c1 106 ASN cc_start: 0.6349 (t0) cc_final: 0.6033 (t0) REVERT: c1 163 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6849 (mm) REVERT: c1 187 THR cc_start: 0.9375 (m) cc_final: 0.9052 (p) REVERT: f1 3 THR cc_start: 0.8713 (p) cc_final: 0.8408 (t) REVERT: f1 43 THR cc_start: 0.8595 (m) cc_final: 0.8390 (p) REVERT: f1 57 GLN cc_start: 0.7623 (mt0) cc_final: 0.7345 (mt0) REVERT: f1 74 ILE cc_start: 0.4971 (tt) cc_final: 0.4707 (tt) REVERT: f1 104 LYS cc_start: 0.8094 (mmmt) cc_final: 0.7350 (pttt) REVERT: f1 135 LEU cc_start: 0.6144 (mt) cc_final: 0.5902 (mt) REVERT: d1 18 LYS cc_start: 0.8279 (tttt) cc_final: 0.7994 (pttm) REVERT: d1 47 ILE cc_start: 0.9366 (mm) cc_final: 0.9148 (tp) REVERT: q1 3 GLN cc_start: 0.8642 (pm20) cc_final: 0.8161 (pm20) REVERT: q1 47 ARG cc_start: 0.8515 (mtt180) cc_final: 0.7147 (mmt180) REVERT: q1 65 GLU cc_start: 0.7417 (tp30) cc_final: 0.7145 (tp30) REVERT: h1 38 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7958 (mp0) REVERT: h1 39 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7357 (mm) REVERT: h1 42 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7823 (tp30) REVERT: h1 43 ARG cc_start: 0.6760 (ttm170) cc_final: 0.6403 (mmm-85) REVERT: a3 53 ASN cc_start: 0.7949 (t0) cc_final: 0.7734 (t0) REVERT: a3 82 MET cc_start: 0.7420 (mtt) cc_final: 0.6784 (mtt) REVERT: a3 113 LEU cc_start: 0.9227 (tp) cc_final: 0.9017 (tt) REVERT: a3 223 TYR cc_start: 0.5463 (t80) cc_final: 0.4896 (p90) REVERT: a3 307 PHE cc_start: 0.8212 (p90) cc_final: 0.8004 (p90) REVERT: a3 369 LEU cc_start: 0.8637 (mt) cc_final: 0.8244 (tt) REVERT: a4 158 HIS cc_start: 0.8613 (OUTLIER) cc_final: 0.7792 (t-90) REVERT: a4 356 ASP cc_start: 0.7657 (m-30) cc_final: 0.7418 (t0) REVERT: a4 402 ILE cc_start: 0.8654 (mt) cc_final: 0.8255 (mt) REVERT: b2 43 LEU cc_start: 0.8876 (tt) cc_final: 0.8384 (mt) REVERT: b2 162 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8399 (mm-30) REVERT: b2 200 LEU cc_start: 0.9299 (tp) cc_final: 0.9038 (tt) REVERT: b2 207 ASN cc_start: 0.8021 (p0) cc_final: 0.7743 (p0) REVERT: b2 263 ASN cc_start: 0.8221 (t0) cc_final: 0.7963 (t0) REVERT: b2 278 TYR cc_start: 0.8527 (t80) cc_final: 0.8130 (t80) REVERT: b2 341 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8256 (mp10) REVERT: b2 365 MET cc_start: 0.8000 (mmm) cc_final: 0.7450 (mtt) REVERT: c2 6 HIS cc_start: 0.8076 (t-90) cc_final: 0.7561 (m-70) REVERT: c2 71 GLN cc_start: 0.7767 (tp40) cc_final: 0.7384 (tp40) REVERT: c2 80 MET cc_start: 0.8053 (OUTLIER) cc_final: 0.7755 (mmm) REVERT: c2 117 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8589 (p) REVERT: c2 178 MET cc_start: 0.8566 (tmm) cc_final: 0.8323 (tmm) REVERT: f2 69 LEU cc_start: 0.8799 (mm) cc_final: 0.8474 (tp) REVERT: f2 71 MET cc_start: 0.5475 (mmt) cc_final: 0.5260 (mmp) REVERT: f2 87 MET cc_start: 0.5251 (ttp) cc_final: 0.5049 (tpt) REVERT: f2 153 PHE cc_start: 0.3820 (m-80) cc_final: 0.3284 (m-80) REVERT: f2 184 SER cc_start: 0.5090 (m) cc_final: 0.4749 (t) REVERT: d2 90 LEU cc_start: 0.9089 (tp) cc_final: 0.8888 (tt) REVERT: q2 2 ARG cc_start: 0.7766 (mtp85) cc_final: 0.6863 (ptt180) REVERT: q2 24 ARG cc_start: 0.7961 (ptp-110) cc_final: 0.7108 (tpt170) REVERT: q2 42 ARG cc_start: 0.7912 (tmt170) cc_final: 0.5539 (mtp85) REVERT: q2 65 GLU cc_start: 0.7044 (tm-30) cc_final: 0.6786 (tm-30) REVERT: h2 59 PHE cc_start: 0.8980 (m-10) cc_final: 0.8596 (m-10) REVERT: i2 13 LEU cc_start: 0.8531 (mm) cc_final: 0.8329 (mp) REVERT: i2 17 THR cc_start: 0.8777 (m) cc_final: 0.8571 (t) REVERT: i2 35 PHE cc_start: 0.8811 (t80) cc_final: 0.8481 (t80) outliers start: 121 outliers final: 67 residues processed: 760 average time/residue: 0.4653 time to fit residues: 569.3870 Evaluate side-chains 654 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 580 time to evaluate : 3.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 127 ILE Chi-restraints excluded: chain a1 residue 134 ILE Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 266 ASP Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 407 VAL Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 180 ASP Chi-restraints excluded: chain a2 residue 186 VAL Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 45 ILE Chi-restraints excluded: chain b1 residue 98 VAL Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 175 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 336 THR Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 42 SER Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 163 ILE Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 55 VAL Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain d1 residue 16 ILE Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 18 THR Chi-restraints excluded: chain h1 residue 39 LEU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 51 LEU Chi-restraints excluded: chain a3 residue 23 LEU Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 304 CYS Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a3 residue 379 ILE Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 351 ASN Chi-restraints excluded: chain b2 residue 42 ILE Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 183 PHE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 282 ARG Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 361 ILE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 80 MET Chi-restraints excluded: chain c2 residue 117 VAL Chi-restraints excluded: chain c2 residue 135 CYS Chi-restraints excluded: chain c2 residue 165 ASN Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 187 THR Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain d2 residue 16 ILE Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 60 THR Chi-restraints excluded: chain h2 residue 39 LEU Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain h2 residue 75 ASN Chi-restraints excluded: chain i2 residue 12 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 196 optimal weight: 3.9990 chunk 109 optimal weight: 0.0170 chunk 294 optimal weight: 5.9990 chunk 240 optimal weight: 5.9990 chunk 97 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 382 optimal weight: 10.0000 chunk 315 optimal weight: 2.9990 chunk 350 optimal weight: 7.9990 chunk 120 optimal weight: 0.1980 chunk 283 optimal weight: 0.6980 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a1 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 312 GLN c1 75 ASN f1 57 GLN a3 141 ASN a3 173 ASN ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a4 174 ASN a4 351 ASN b2 267 HIS b2 312 GLN ** c2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 121 HIS c2 180 GLN ** d2 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q2 6 HIS i2 54 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.3277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 32785 Z= 0.249 Angle : 0.706 17.172 44538 Z= 0.342 Chirality : 0.044 0.179 4837 Planarity : 0.005 0.066 5675 Dihedral : 11.711 144.418 4740 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.83 % Allowed : 14.62 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.13), residues: 3883 helix: 0.40 (0.11), residues: 2006 sheet: -0.70 (0.26), residues: 375 loop : -2.43 (0.15), residues: 1502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPa3 443 HIS 0.010 0.001 HISa1 252 PHE 0.015 0.001 PHEi2 31 TYR 0.019 0.001 TYRc1 164 ARG 0.006 0.001 ARGa3 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 782 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 621 time to evaluate : 4.126 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: a1 60 GLU cc_start: 0.8739 (tt0) cc_final: 0.8392 (tt0) REVERT: a1 130 GLU cc_start: 0.8236 (mm-30) cc_final: 0.7644 (tp30) REVERT: a1 329 MET cc_start: 0.8493 (mmm) cc_final: 0.8199 (tpt) REVERT: a2 90 GLU cc_start: 0.8287 (mp0) cc_final: 0.8044 (mp0) REVERT: a2 99 THR cc_start: 0.8855 (OUTLIER) cc_final: 0.8620 (p) REVERT: a2 206 LEU cc_start: 0.8870 (tp) cc_final: 0.8607 (tt) REVERT: b1 121 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: b1 138 MET cc_start: 0.7412 (tpp) cc_final: 0.7013 (tpp) REVERT: b1 237 LEU cc_start: 0.8551 (pp) cc_final: 0.8278 (mt) REVERT: b1 240 MET cc_start: 0.8483 (mmp) cc_final: 0.8144 (mmm) REVERT: b1 243 VAL cc_start: 0.9077 (m) cc_final: 0.8756 (m) REVERT: b1 252 ASP cc_start: 0.7816 (p0) cc_final: 0.7287 (p0) REVERT: b1 254 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8052 (p0) REVERT: c1 106 ASN cc_start: 0.6428 (t0) cc_final: 0.6155 (t0) REVERT: c1 187 THR cc_start: 0.9357 (m) cc_final: 0.9051 (p) REVERT: c1 224 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.7964 (t-90) REVERT: f1 3 THR cc_start: 0.8948 (p) cc_final: 0.8585 (t) REVERT: f1 57 GLN cc_start: 0.7751 (mt0) cc_final: 0.7505 (mt0) REVERT: f1 74 ILE cc_start: 0.5185 (tt) cc_final: 0.4963 (tt) REVERT: f1 104 LYS cc_start: 0.8081 (mmmt) cc_final: 0.7342 (pttt) REVERT: d1 18 LYS cc_start: 0.8200 (tttt) cc_final: 0.7980 (pttt) REVERT: d1 47 ILE cc_start: 0.9432 (mm) cc_final: 0.9195 (tp) REVERT: q1 3 GLN cc_start: 0.8388 (pm20) cc_final: 0.8013 (pm20) REVERT: q1 47 ARG cc_start: 0.8552 (mtt180) cc_final: 0.7220 (mmt180) REVERT: h1 38 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8039 (mt-10) REVERT: h1 39 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7786 (mm) REVERT: h1 42 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.7903 (tp30) REVERT: h1 43 ARG cc_start: 0.6802 (ttm170) cc_final: 0.6402 (mmm-85) REVERT: a3 82 MET cc_start: 0.7341 (mtt) cc_final: 0.6784 (mtt) REVERT: a3 145 MET cc_start: 0.8010 (mtm) cc_final: 0.7538 (ttm) REVERT: a3 223 TYR cc_start: 0.5498 (t80) cc_final: 0.4899 (p90) REVERT: a3 307 PHE cc_start: 0.8394 (p90) cc_final: 0.8121 (p90) REVERT: a3 343 MET cc_start: 0.9006 (mmp) cc_final: 0.8684 (mmp) REVERT: a3 369 LEU cc_start: 0.8717 (mt) cc_final: 0.8232 (tt) REVERT: a4 158 HIS cc_start: 0.8604 (OUTLIER) cc_final: 0.7885 (t-90) REVERT: a4 338 LYS cc_start: 0.9308 (mttt) cc_final: 0.9018 (mmmt) REVERT: a4 356 ASP cc_start: 0.7674 (m-30) cc_final: 0.7399 (t0) REVERT: b2 43 LEU cc_start: 0.8784 (tt) cc_final: 0.8260 (mt) REVERT: b2 129 MET cc_start: 0.8675 (mtm) cc_final: 0.8236 (mtm) REVERT: b2 162 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8351 (mm-30) REVERT: b2 200 LEU cc_start: 0.9326 (tp) cc_final: 0.9080 (tt) REVERT: b2 206 ASN cc_start: 0.8877 (t0) cc_final: 0.8667 (t0) REVERT: b2 207 ASN cc_start: 0.8331 (p0) cc_final: 0.7937 (p0) REVERT: b2 263 ASN cc_start: 0.8248 (t0) cc_final: 0.7862 (t0) REVERT: b2 278 TYR cc_start: 0.8543 (t80) cc_final: 0.8082 (t80) REVERT: b2 316 MET cc_start: 0.7543 (ttm) cc_final: 0.6843 (mtp) REVERT: b2 365 MET cc_start: 0.7961 (mmm) cc_final: 0.7363 (mtt) REVERT: c2 6 HIS cc_start: 0.8115 (t-90) cc_final: 0.7567 (m-70) REVERT: c2 71 GLN cc_start: 0.7701 (tp40) cc_final: 0.7393 (tp40) REVERT: c2 80 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.7656 (mmt) REVERT: c2 117 VAL cc_start: 0.8802 (OUTLIER) cc_final: 0.8554 (p) REVERT: c2 152 PHE cc_start: 0.8363 (t80) cc_final: 0.8082 (t80) REVERT: c2 178 MET cc_start: 0.8728 (tmm) cc_final: 0.8451 (tmm) REVERT: f2 69 LEU cc_start: 0.8841 (mm) cc_final: 0.8457 (tp) REVERT: f2 87 MET cc_start: 0.5463 (ttp) cc_final: 0.5135 (tpt) REVERT: f2 153 PHE cc_start: 0.4217 (m-80) cc_final: 0.3619 (m-80) REVERT: d2 45 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7159 (tt0) REVERT: q2 2 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7027 (ptt180) REVERT: q2 42 ARG cc_start: 0.7844 (tmt170) cc_final: 0.5455 (mtp85) REVERT: h2 59 PHE cc_start: 0.8966 (m-10) cc_final: 0.8567 (m-10) REVERT: i2 8 ARG cc_start: 0.8686 (ptt-90) cc_final: 0.8269 (ptp-170) REVERT: i2 16 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7950 (mmm-85) REVERT: i2 44 GLU cc_start: 0.7319 (tp30) cc_final: 0.6593 (tm-30) outliers start: 161 outliers final: 105 residues processed: 715 average time/residue: 0.4124 time to fit residues: 478.6596 Evaluate side-chains 679 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 565 time to evaluate : 3.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 35 CYS Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 234 CYS Chi-restraints excluded: chain a1 residue 266 ASP Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 437 ILE Chi-restraints excluded: chain a2 residue 99 THR Chi-restraints excluded: chain a2 residue 100 SER Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 180 ASP Chi-restraints excluded: chain a2 residue 186 VAL Chi-restraints excluded: chain a2 residue 374 SER Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 225 THR Chi-restraints excluded: chain b1 residue 254 ASP Chi-restraints excluded: chain b1 residue 283 SER Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 336 THR Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 55 VAL Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 18 THR Chi-restraints excluded: chain h1 residue 39 LEU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 40 ASP Chi-restraints excluded: chain i1 residue 51 LEU Chi-restraints excluded: chain a3 residue 23 LEU Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 240 GLU Chi-restraints excluded: chain a3 residue 264 ASN Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 304 CYS Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a3 residue 379 ILE Chi-restraints excluded: chain a4 residue 51 ILE Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 100 SER Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 116 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 207 ILE Chi-restraints excluded: chain a4 residue 225 ASN Chi-restraints excluded: chain a4 residue 351 ASN Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain a4 residue 397 THR Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 42 ILE Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 133 LEU Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 234 LEU Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 282 ARG Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 349 ILE Chi-restraints excluded: chain b2 residue 361 ILE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 80 MET Chi-restraints excluded: chain c2 residue 117 VAL Chi-restraints excluded: chain c2 residue 135 CYS Chi-restraints excluded: chain c2 residue 157 ILE Chi-restraints excluded: chain c2 residue 165 ASN Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 187 THR Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain f2 residue 47 VAL Chi-restraints excluded: chain d2 residue 16 ILE Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain d2 residue 81 THR Chi-restraints excluded: chain d2 residue 94 LEU Chi-restraints excluded: chain d2 residue 98 ILE Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 46 LEU Chi-restraints excluded: chain q2 residue 60 THR Chi-restraints excluded: chain h2 residue 39 LEU Chi-restraints excluded: chain h2 residue 53 ASP Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain h2 residue 75 ASN Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 349 optimal weight: 0.0870 chunk 266 optimal weight: 3.9990 chunk 183 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 237 optimal weight: 3.9990 chunk 355 optimal weight: 10.0000 chunk 376 optimal weight: 7.9990 chunk 185 optimal weight: 4.9990 chunk 336 optimal weight: 3.9990 chunk 101 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a1 323 HIS a1 328 HIS ** a2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 312 GLN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h1 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a4 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 8 HIS ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 121 HIS ** d2 73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32785 Z= 0.185 Angle : 0.660 15.815 44538 Z= 0.318 Chirality : 0.042 0.192 4837 Planarity : 0.005 0.063 5675 Dihedral : 11.212 150.473 4738 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.54 % Rotamer: Outliers : 4.38 % Allowed : 15.95 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3883 helix: 0.74 (0.12), residues: 2024 sheet: -0.57 (0.26), residues: 377 loop : -2.31 (0.16), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRPi1 52 HIS 0.011 0.001 HISc2 121 PHE 0.020 0.001 PHEq2 55 TYR 0.022 0.001 TYRi1 43 ARG 0.007 0.000 ARGh2 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 633 time to evaluate : 3.602 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: a1 60 GLU cc_start: 0.8754 (tt0) cc_final: 0.8060 (tt0) REVERT: a1 115 ASP cc_start: 0.7453 (t0) cc_final: 0.6965 (t0) REVERT: a1 130 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7629 (tp30) REVERT: a1 153 LEU cc_start: 0.9380 (tp) cc_final: 0.8998 (tt) REVERT: a1 271 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7957 (tp-100) REVERT: a1 327 ASP cc_start: 0.8321 (t70) cc_final: 0.7945 (p0) REVERT: a1 329 MET cc_start: 0.8510 (mmm) cc_final: 0.8076 (tpt) REVERT: a2 90 GLU cc_start: 0.8326 (mp0) cc_final: 0.7990 (mp0) REVERT: b1 121 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.7377 (m-10) REVERT: b1 138 MET cc_start: 0.7264 (tpp) cc_final: 0.6793 (tpp) REVERT: b1 240 MET cc_start: 0.8468 (mmp) cc_final: 0.8100 (mmm) REVERT: b1 243 VAL cc_start: 0.9011 (m) cc_final: 0.8717 (m) REVERT: b1 252 ASP cc_start: 0.7812 (p0) cc_final: 0.7220 (p0) REVERT: b1 254 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.8153 (p0) REVERT: b1 282 ARG cc_start: 0.9103 (ttp-110) cc_final: 0.8448 (ttp-110) REVERT: b1 328 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8494 (tt) REVERT: c1 55 CYS cc_start: 0.8708 (p) cc_final: 0.8443 (p) REVERT: c1 106 ASN cc_start: 0.6515 (t0) cc_final: 0.6268 (t0) REVERT: c1 187 THR cc_start: 0.9389 (m) cc_final: 0.9067 (p) REVERT: c1 211 MET cc_start: 0.7303 (mmt) cc_final: 0.6770 (tmm) REVERT: c1 224 HIS cc_start: 0.8301 (OUTLIER) cc_final: 0.7924 (t-90) REVERT: f1 3 THR cc_start: 0.8853 (p) cc_final: 0.8566 (t) REVERT: f1 104 LYS cc_start: 0.8126 (mmmt) cc_final: 0.7388 (pttt) REVERT: f1 135 LEU cc_start: 0.6144 (mt) cc_final: 0.5780 (mm) REVERT: d1 34 ASP cc_start: 0.8536 (p0) cc_final: 0.8293 (p0) REVERT: d1 47 ILE cc_start: 0.9385 (mm) cc_final: 0.9180 (tp) REVERT: q1 3 GLN cc_start: 0.8347 (pm20) cc_final: 0.7726 (pm20) REVERT: q1 47 ARG cc_start: 0.8507 (mtt180) cc_final: 0.7077 (mmt180) REVERT: h1 18 THR cc_start: 0.8126 (OUTLIER) cc_final: 0.7925 (m) REVERT: h1 38 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8068 (mp0) REVERT: h1 42 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7890 (tp30) REVERT: i1 37 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8311 (mm-40) REVERT: i1 43 TYR cc_start: 0.8308 (t80) cc_final: 0.8087 (t80) REVERT: a3 82 MET cc_start: 0.7200 (mtt) cc_final: 0.6702 (mtt) REVERT: a3 89 TYR cc_start: 0.8124 (p90) cc_final: 0.7898 (p90) REVERT: a3 145 MET cc_start: 0.7934 (mtm) cc_final: 0.7596 (ttm) REVERT: a3 223 TYR cc_start: 0.5376 (t80) cc_final: 0.4790 (p90) REVERT: a3 369 LEU cc_start: 0.8652 (mt) cc_final: 0.8153 (tt) REVERT: a4 68 LEU cc_start: 0.9360 (tp) cc_final: 0.9005 (tp) REVERT: a4 158 HIS cc_start: 0.8504 (OUTLIER) cc_final: 0.7823 (t-90) REVERT: a4 338 LYS cc_start: 0.9262 (mttt) cc_final: 0.9043 (mmmt) REVERT: a4 356 ASP cc_start: 0.7629 (m-30) cc_final: 0.7357 (t0) REVERT: b2 12 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8587 (ttmm) REVERT: b2 43 LEU cc_start: 0.8756 (tt) cc_final: 0.8306 (mt) REVERT: b2 91 PHE cc_start: 0.8442 (m-80) cc_final: 0.8126 (m-10) REVERT: b2 121 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.7052 (m-80) REVERT: b2 124 MET cc_start: 0.7880 (mtm) cc_final: 0.7665 (mtm) REVERT: b2 129 MET cc_start: 0.8639 (mtm) cc_final: 0.8353 (mtp) REVERT: b2 200 LEU cc_start: 0.9243 (tp) cc_final: 0.8993 (tt) REVERT: b2 207 ASN cc_start: 0.8167 (p0) cc_final: 0.7777 (p0) REVERT: b2 263 ASN cc_start: 0.8174 (t0) cc_final: 0.7778 (t0) REVERT: b2 316 MET cc_start: 0.7525 (ttm) cc_final: 0.6703 (mtp) REVERT: b2 341 GLN cc_start: 0.8734 (mm-40) cc_final: 0.8527 (mp10) REVERT: c2 6 HIS cc_start: 0.8312 (t-90) cc_final: 0.7605 (m-70) REVERT: c2 80 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7577 (mmt) REVERT: c2 152 PHE cc_start: 0.8264 (t80) cc_final: 0.8044 (t80) REVERT: c2 178 MET cc_start: 0.8728 (tmm) cc_final: 0.8455 (tmm) REVERT: f2 17 GLU cc_start: 0.8022 (pm20) cc_final: 0.7350 (tp30) REVERT: f2 69 LEU cc_start: 0.8864 (mm) cc_final: 0.8414 (tp) REVERT: f2 87 MET cc_start: 0.5480 (ttp) cc_final: 0.5183 (tpt) REVERT: f2 153 PHE cc_start: 0.4281 (m-80) cc_final: 0.3557 (m-80) REVERT: f2 184 SER cc_start: 0.4977 (m) cc_final: 0.4713 (t) REVERT: d2 45 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7188 (tt0) REVERT: q2 2 ARG cc_start: 0.7811 (mtp85) cc_final: 0.7009 (ptt180) REVERT: q2 42 ARG cc_start: 0.7631 (tmt170) cc_final: 0.5134 (mtp85) REVERT: q2 71 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7740 (mtm-85) REVERT: h2 59 PHE cc_start: 0.8842 (m-10) cc_final: 0.8508 (m-10) REVERT: i2 8 ARG cc_start: 0.8674 (ptt-90) cc_final: 0.8301 (ptp-170) REVERT: i2 35 PHE cc_start: 0.8645 (t80) cc_final: 0.8431 (t80) REVERT: i2 44 GLU cc_start: 0.7018 (tp30) cc_final: 0.6319 (tm-30) outliers start: 146 outliers final: 94 residues processed: 724 average time/residue: 0.4469 time to fit residues: 532.1694 Evaluate side-chains 670 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 566 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 219 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 266 ASP Chi-restraints excluded: chain a1 residue 323 HIS Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 437 ILE Chi-restraints excluded: chain a2 residue 100 SER Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 180 ASP Chi-restraints excluded: chain a2 residue 186 VAL Chi-restraints excluded: chain a2 residue 374 SER Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 78 ILE Chi-restraints excluded: chain b1 residue 92 ILE Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 254 ASP Chi-restraints excluded: chain b1 residue 292 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 328 LEU Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 131 LEU Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 18 THR Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 40 ASP Chi-restraints excluded: chain i1 residue 51 LEU Chi-restraints excluded: chain a3 residue 23 LEU Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 264 ASN Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a4 residue 51 ILE Chi-restraints excluded: chain a4 residue 100 SER Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 116 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 207 ILE Chi-restraints excluded: chain a4 residue 364 LEU Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain a4 residue 397 THR Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 42 ILE Chi-restraints excluded: chain b2 residue 56 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 121 PHE Chi-restraints excluded: chain b2 residue 133 LEU Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 234 LEU Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 282 ARG Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 361 ILE Chi-restraints excluded: chain b2 residue 363 LEU Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 80 MET Chi-restraints excluded: chain c2 residue 135 CYS Chi-restraints excluded: chain c2 residue 165 ASN Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain c2 residue 208 LEU Chi-restraints excluded: chain f2 residue 19 LEU Chi-restraints excluded: chain f2 residue 47 VAL Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain d2 residue 94 LEU Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 46 LEU Chi-restraints excluded: chain q2 residue 71 ARG Chi-restraints excluded: chain q2 residue 73 ASN Chi-restraints excluded: chain h2 residue 39 LEU Chi-restraints excluded: chain h2 residue 40 CYS Chi-restraints excluded: chain h2 residue 53 ASP Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain h2 residue 75 ASN Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 313 optimal weight: 1.9990 chunk 213 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 chunk 155 optimal weight: 0.0470 chunk 320 optimal weight: 7.9990 chunk 259 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 337 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 overall best weight: 2.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 264 ASN ** a1 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a2 277 HIS ** a2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1 312 GLN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 57 GLN ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 8 HIS b2 137 GLN ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 121 HIS d2 73 GLN q2 6 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 32785 Z= 0.311 Angle : 0.723 16.617 44538 Z= 0.349 Chirality : 0.044 0.224 4837 Planarity : 0.005 0.077 5675 Dihedral : 11.156 153.373 4738 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.34 % Favored : 92.63 % Rotamer: Outliers : 5.08 % Allowed : 16.67 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.14), residues: 3883 helix: 0.91 (0.12), residues: 1997 sheet: -0.53 (0.26), residues: 389 loop : -2.19 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPa3 443 HIS 0.015 0.001 HISa1 323 PHE 0.039 0.002 PHEb1 276 TYR 0.021 0.002 TYRb2 358 ARG 0.006 0.001 ARGb1 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 584 time to evaluate : 4.015 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: a1 60 GLU cc_start: 0.8909 (tt0) cc_final: 0.8284 (tt0) REVERT: a1 115 ASP cc_start: 0.7461 (t0) cc_final: 0.7112 (t0) REVERT: a1 130 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7633 (tp30) REVERT: a1 271 GLN cc_start: 0.8308 (tp-100) cc_final: 0.8065 (tp-100) REVERT: a1 327 ASP cc_start: 0.8311 (t70) cc_final: 0.8007 (p0) REVERT: a1 329 MET cc_start: 0.8529 (mmm) cc_final: 0.8191 (tpt) REVERT: a2 90 GLU cc_start: 0.8444 (mp0) cc_final: 0.8060 (mp0) REVERT: a2 99 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8600 (p) REVERT: b1 8 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7395 (t70) REVERT: b1 35 SER cc_start: 0.8833 (p) cc_final: 0.8191 (t) REVERT: b1 121 PHE cc_start: 0.7686 (OUTLIER) cc_final: 0.7456 (m-10) REVERT: b1 138 MET cc_start: 0.7622 (tpp) cc_final: 0.7050 (tpp) REVERT: b1 240 MET cc_start: 0.8472 (mmp) cc_final: 0.7835 (mmm) REVERT: b1 243 VAL cc_start: 0.9057 (m) cc_final: 0.8763 (m) REVERT: b1 328 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8486 (tt) REVERT: b1 366 MET cc_start: 0.8982 (tpp) cc_final: 0.8719 (tpp) REVERT: c1 55 CYS cc_start: 0.8729 (p) cc_final: 0.8427 (p) REVERT: c1 106 ASN cc_start: 0.6638 (t0) cc_final: 0.6215 (t0) REVERT: c1 109 LEU cc_start: 0.9030 (tp) cc_final: 0.8503 (pt) REVERT: c1 187 THR cc_start: 0.9424 (m) cc_final: 0.9093 (p) REVERT: c1 210 MET cc_start: 0.8166 (mmm) cc_final: 0.7946 (tpt) REVERT: c1 211 MET cc_start: 0.7400 (mmt) cc_final: 0.6983 (tmm) REVERT: c1 224 HIS cc_start: 0.8407 (OUTLIER) cc_final: 0.8050 (t-90) REVERT: f1 3 THR cc_start: 0.8970 (p) cc_final: 0.8571 (t) REVERT: f1 87 MET cc_start: 0.4368 (tpp) cc_final: 0.4150 (tpt) REVERT: f1 104 LYS cc_start: 0.8266 (mmmt) cc_final: 0.7476 (pttt) REVERT: f1 135 LEU cc_start: 0.6153 (mt) cc_final: 0.5949 (mt) REVERT: d1 34 ASP cc_start: 0.8675 (p0) cc_final: 0.8468 (p0) REVERT: d1 47 ILE cc_start: 0.9440 (mm) cc_final: 0.9210 (tp) REVERT: q1 3 GLN cc_start: 0.8408 (pm20) cc_final: 0.7806 (pm20) REVERT: q1 22 GLU cc_start: 0.7974 (tp30) cc_final: 0.7659 (tp30) REVERT: q1 47 ARG cc_start: 0.8631 (mtt180) cc_final: 0.7265 (mmt180) REVERT: q1 65 GLU cc_start: 0.7995 (tp30) cc_final: 0.7573 (tp30) REVERT: h1 38 GLU cc_start: 0.8337 (mt-10) cc_final: 0.8093 (mt-10) REVERT: h1 42 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8014 (tp30) REVERT: i1 43 TYR cc_start: 0.8399 (t80) cc_final: 0.8197 (t80) REVERT: a3 19 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7538 (mm) REVERT: a3 82 MET cc_start: 0.7416 (mtt) cc_final: 0.6937 (mtt) REVERT: a3 145 MET cc_start: 0.7936 (mtm) cc_final: 0.7673 (ttm) REVERT: a3 329 MET cc_start: 0.8651 (mmm) cc_final: 0.8065 (mmt) REVERT: a3 375 VAL cc_start: 0.8927 (m) cc_final: 0.8608 (p) REVERT: a4 68 LEU cc_start: 0.9473 (tp) cc_final: 0.9131 (tp) REVERT: a4 158 HIS cc_start: 0.8601 (OUTLIER) cc_final: 0.8044 (t-90) REVERT: a4 356 ASP cc_start: 0.7642 (m-30) cc_final: 0.7352 (t0) REVERT: b2 12 LYS cc_start: 0.8871 (ttmt) cc_final: 0.8573 (ttmm) REVERT: b2 43 LEU cc_start: 0.8771 (tt) cc_final: 0.8294 (mt) REVERT: b2 91 PHE cc_start: 0.8490 (m-80) cc_final: 0.8133 (m-80) REVERT: b2 129 MET cc_start: 0.8687 (mtm) cc_final: 0.8454 (mtp) REVERT: b2 240 MET cc_start: 0.8093 (mmt) cc_final: 0.7846 (mmp) REVERT: b2 263 ASN cc_start: 0.8266 (t0) cc_final: 0.7879 (t0) REVERT: b2 269 LYS cc_start: 0.8704 (pptt) cc_final: 0.8475 (pptt) REVERT: b2 316 MET cc_start: 0.7752 (ttm) cc_final: 0.7449 (mtp) REVERT: c2 6 HIS cc_start: 0.8223 (t-90) cc_final: 0.7673 (m-70) REVERT: c2 178 MET cc_start: 0.8794 (tmm) cc_final: 0.8536 (tmm) REVERT: f2 17 GLU cc_start: 0.8029 (pm20) cc_final: 0.7359 (tp30) REVERT: f2 69 LEU cc_start: 0.8877 (mm) cc_final: 0.8409 (tp) REVERT: f2 87 MET cc_start: 0.5597 (ttp) cc_final: 0.5261 (tpt) REVERT: f2 184 SER cc_start: 0.4945 (m) cc_final: 0.4697 (t) REVERT: q2 2 ARG cc_start: 0.7725 (mtp85) cc_final: 0.6907 (ptt180) REVERT: q2 3 GLN cc_start: 0.7944 (tt0) cc_final: 0.7727 (tt0) REVERT: q2 42 ARG cc_start: 0.7741 (tmt170) cc_final: 0.5160 (mtp85) REVERT: q2 71 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7815 (mtm-85) REVERT: h2 59 PHE cc_start: 0.8929 (m-10) cc_final: 0.8593 (m-10) REVERT: h2 73 LEU cc_start: 0.8577 (tt) cc_final: 0.8272 (tp) REVERT: i2 8 ARG cc_start: 0.8748 (ptt-90) cc_final: 0.8516 (ptp-170) REVERT: i2 35 PHE cc_start: 0.8645 (t80) cc_final: 0.8367 (t80) outliers start: 169 outliers final: 125 residues processed: 685 average time/residue: 0.4101 time to fit residues: 458.6880 Evaluate side-chains 672 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 538 time to evaluate : 3.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 134 ILE Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 161 THR Chi-restraints excluded: chain a1 residue 167 VAL Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 219 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 234 CYS Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 266 ASP Chi-restraints excluded: chain a1 residue 323 HIS Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 437 ILE Chi-restraints excluded: chain a2 residue 99 THR Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 180 ASP Chi-restraints excluded: chain a2 residue 186 VAL Chi-restraints excluded: chain a2 residue 374 SER Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 12 LYS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 46 LEU Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 72 ASP Chi-restraints excluded: chain b1 residue 78 ILE Chi-restraints excluded: chain b1 residue 92 ILE Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 225 THR Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 328 LEU Chi-restraints excluded: chain b1 residue 334 THR Chi-restraints excluded: chain b1 residue 336 THR Chi-restraints excluded: chain b1 residue 353 LEU Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 42 SER Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 131 LEU Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 177 THR Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 38 LEU Chi-restraints excluded: chain f1 residue 55 VAL Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 18 THR Chi-restraints excluded: chain h1 residue 39 LEU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 40 ASP Chi-restraints excluded: chain i1 residue 51 LEU Chi-restraints excluded: chain a3 residue 19 LEU Chi-restraints excluded: chain a3 residue 23 LEU Chi-restraints excluded: chain a3 residue 100 LYS Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 240 GLU Chi-restraints excluded: chain a3 residue 264 ASN Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 304 CYS Chi-restraints excluded: chain a3 residue 320 LEU Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a4 residue 51 ILE Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 100 SER Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 116 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 186 VAL Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 225 ASN Chi-restraints excluded: chain a4 residue 364 LEU Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain a4 residue 397 THR Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 42 ILE Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 126 THR Chi-restraints excluded: chain b2 residue 171 ASP Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 282 ARG Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 331 ASP Chi-restraints excluded: chain b2 residue 363 LEU Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 127 VAL Chi-restraints excluded: chain c2 residue 135 CYS Chi-restraints excluded: chain c2 residue 157 ILE Chi-restraints excluded: chain c2 residue 165 ASN Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 187 THR Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain f2 residue 12 ASP Chi-restraints excluded: chain f2 residue 19 LEU Chi-restraints excluded: chain f2 residue 47 VAL Chi-restraints excluded: chain f2 residue 131 GLU Chi-restraints excluded: chain f2 residue 193 VAL Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain d2 residue 107 TRP Chi-restraints excluded: chain d2 residue 108 THR Chi-restraints excluded: chain q2 residue 18 LEU Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 46 LEU Chi-restraints excluded: chain q2 residue 60 THR Chi-restraints excluded: chain q2 residue 71 ARG Chi-restraints excluded: chain h2 residue 39 LEU Chi-restraints excluded: chain h2 residue 40 CYS Chi-restraints excluded: chain h2 residue 41 ASP Chi-restraints excluded: chain h2 residue 53 ASP Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain h2 residue 75 ASN Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 126 optimal weight: 8.9990 chunk 338 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 220 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 376 optimal weight: 8.9990 chunk 312 optimal weight: 0.0270 chunk 174 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 overall best weight: 2.0044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 323 HIS a2 305 GLN ** a2 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 57 GLN ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 8 HIS ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i2 47 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 32785 Z= 0.307 Angle : 0.721 16.300 44538 Z= 0.348 Chirality : 0.044 0.221 4837 Planarity : 0.005 0.069 5675 Dihedral : 11.032 153.348 4738 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.31 % Favored : 92.66 % Rotamer: Outliers : 5.47 % Allowed : 17.06 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.14), residues: 3883 helix: 0.96 (0.12), residues: 1999 sheet: -0.58 (0.26), residues: 380 loop : -2.11 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPa3 443 HIS 0.008 0.001 HISb1 196 PHE 0.031 0.002 PHEb1 276 TYR 0.018 0.002 TYRq1 56 ARG 0.005 0.001 ARGa3 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 742 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 560 time to evaluate : 3.723 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: a1 60 GLU cc_start: 0.8915 (tt0) cc_final: 0.8325 (tt0) REVERT: a1 82 MET cc_start: 0.8066 (tpp) cc_final: 0.7840 (tpt) REVERT: a1 115 ASP cc_start: 0.7497 (t0) cc_final: 0.7107 (t0) REVERT: a1 130 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7621 (tp30) REVERT: a1 271 GLN cc_start: 0.8321 (tp-100) cc_final: 0.8092 (tp-100) REVERT: a1 327 ASP cc_start: 0.8291 (t70) cc_final: 0.8021 (p0) REVERT: a1 329 MET cc_start: 0.8498 (mmm) cc_final: 0.8190 (tpt) REVERT: a2 90 GLU cc_start: 0.8511 (mp0) cc_final: 0.7957 (mp0) REVERT: a2 99 THR cc_start: 0.8857 (OUTLIER) cc_final: 0.8609 (p) REVERT: b1 8 HIS cc_start: 0.7930 (OUTLIER) cc_final: 0.7291 (t70) REVERT: b1 35 SER cc_start: 0.8798 (p) cc_final: 0.8546 (t) REVERT: b1 96 MET cc_start: 0.7723 (mmm) cc_final: 0.7380 (mtt) REVERT: b1 121 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7619 (m-10) REVERT: b1 240 MET cc_start: 0.8479 (mmp) cc_final: 0.7836 (mmm) REVERT: b1 243 VAL cc_start: 0.9080 (m) cc_final: 0.8725 (m) REVERT: c1 55 CYS cc_start: 0.8574 (p) cc_final: 0.8264 (p) REVERT: c1 106 ASN cc_start: 0.6674 (t0) cc_final: 0.6256 (t0) REVERT: c1 109 LEU cc_start: 0.9103 (tp) cc_final: 0.8584 (pt) REVERT: c1 178 MET cc_start: 0.7627 (mmp) cc_final: 0.7195 (tpp) REVERT: c1 187 THR cc_start: 0.9452 (m) cc_final: 0.9132 (p) REVERT: c1 211 MET cc_start: 0.7436 (mmt) cc_final: 0.7134 (tmm) REVERT: c1 224 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.8119 (t-90) REVERT: f1 3 THR cc_start: 0.8826 (p) cc_final: 0.8494 (t) REVERT: f1 104 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7460 (pttt) REVERT: q1 3 GLN cc_start: 0.8408 (pm20) cc_final: 0.7799 (pm20) REVERT: q1 22 GLU cc_start: 0.7869 (tp30) cc_final: 0.7498 (tp30) REVERT: q1 47 ARG cc_start: 0.8694 (mtt180) cc_final: 0.7227 (mmt180) REVERT: q1 65 GLU cc_start: 0.8072 (tp30) cc_final: 0.7681 (tp30) REVERT: h1 13 LEU cc_start: 0.7554 (OUTLIER) cc_final: 0.7023 (tm) REVERT: h1 38 GLU cc_start: 0.8303 (mt-10) cc_final: 0.8096 (mp0) REVERT: h1 42 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8072 (tp30) REVERT: a3 19 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7436 (mm) REVERT: a3 82 MET cc_start: 0.7455 (mtt) cc_final: 0.7097 (mtt) REVERT: a3 245 GLU cc_start: 0.8253 (tp30) cc_final: 0.7588 (tm-30) REVERT: a3 329 MET cc_start: 0.8739 (mmm) cc_final: 0.8252 (mmt) REVERT: a3 369 LEU cc_start: 0.8549 (mp) cc_final: 0.8029 (tt) REVERT: a3 375 VAL cc_start: 0.8993 (m) cc_final: 0.8729 (p) REVERT: a4 68 LEU cc_start: 0.9490 (tp) cc_final: 0.9128 (tp) REVERT: a4 158 HIS cc_start: 0.8630 (OUTLIER) cc_final: 0.8031 (t-90) REVERT: b2 12 LYS cc_start: 0.8889 (ttmt) cc_final: 0.8568 (ttmm) REVERT: b2 43 LEU cc_start: 0.8814 (tt) cc_final: 0.8343 (mt) REVERT: b2 91 PHE cc_start: 0.8549 (m-80) cc_final: 0.8184 (m-80) REVERT: b2 129 MET cc_start: 0.8695 (mtm) cc_final: 0.8462 (mtp) REVERT: b2 263 ASN cc_start: 0.8234 (t0) cc_final: 0.7827 (t0) REVERT: b2 316 MET cc_start: 0.7834 (ttm) cc_final: 0.7503 (mtp) REVERT: f2 17 GLU cc_start: 0.8057 (pm20) cc_final: 0.7312 (tp30) REVERT: f2 18 VAL cc_start: 0.8065 (OUTLIER) cc_final: 0.7763 (t) REVERT: f2 69 LEU cc_start: 0.8889 (mm) cc_final: 0.8395 (tp) REVERT: f2 87 MET cc_start: 0.5428 (ttp) cc_final: 0.5189 (tpt) REVERT: f2 96 LEU cc_start: 0.6071 (tt) cc_final: 0.5603 (mp) REVERT: f2 184 SER cc_start: 0.4965 (m) cc_final: 0.4727 (t) REVERT: q2 2 ARG cc_start: 0.7785 (mtp85) cc_final: 0.6939 (ptt180) REVERT: q2 3 GLN cc_start: 0.8007 (tt0) cc_final: 0.7776 (tt0) REVERT: q2 42 ARG cc_start: 0.7803 (tmt170) cc_final: 0.5333 (mtp85) REVERT: h2 52 GLU cc_start: 0.8354 (tm-30) cc_final: 0.7967 (tm-30) REVERT: h2 59 PHE cc_start: 0.8879 (m-10) cc_final: 0.8515 (m-10) REVERT: h2 73 LEU cc_start: 0.8636 (tt) cc_final: 0.8384 (tp) REVERT: i2 35 PHE cc_start: 0.8688 (t80) cc_final: 0.8476 (t80) outliers start: 182 outliers final: 139 residues processed: 668 average time/residue: 0.3977 time to fit residues: 436.2705 Evaluate side-chains 682 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 534 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 4 TYR Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 116 ILE Chi-restraints excluded: chain a1 residue 134 ILE Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 161 THR Chi-restraints excluded: chain a1 residue 167 VAL Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 219 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 234 CYS Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 266 ASP Chi-restraints excluded: chain a1 residue 323 HIS Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 437 ILE Chi-restraints excluded: chain a2 residue 99 THR Chi-restraints excluded: chain a2 residue 100 SER Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 176 LEU Chi-restraints excluded: chain a2 residue 180 ASP Chi-restraints excluded: chain a2 residue 186 VAL Chi-restraints excluded: chain a2 residue 374 SER Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 12 LYS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 72 ASP Chi-restraints excluded: chain b1 residue 78 ILE Chi-restraints excluded: chain b1 residue 92 ILE Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 214 ASP Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 225 THR Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 334 THR Chi-restraints excluded: chain b1 residue 336 THR Chi-restraints excluded: chain b1 residue 353 LEU Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 42 SER Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 97 ASN Chi-restraints excluded: chain c1 residue 131 LEU Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 177 THR Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 55 VAL Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 13 LEU Chi-restraints excluded: chain h1 residue 18 THR Chi-restraints excluded: chain h1 residue 39 LEU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 55 THR Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 40 ASP Chi-restraints excluded: chain i1 residue 51 LEU Chi-restraints excluded: chain a3 residue 19 LEU Chi-restraints excluded: chain a3 residue 23 LEU Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 240 GLU Chi-restraints excluded: chain a3 residue 264 ASN Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 288 MET Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 304 CYS Chi-restraints excluded: chain a3 residue 320 LEU Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a4 residue 20 HIS Chi-restraints excluded: chain a4 residue 51 ILE Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 116 VAL Chi-restraints excluded: chain a4 residue 126 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 186 VAL Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 225 ASN Chi-restraints excluded: chain a4 residue 364 LEU Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain a4 residue 397 THR Chi-restraints excluded: chain b2 residue 28 SER Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 42 ILE Chi-restraints excluded: chain b2 residue 67 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 171 ASP Chi-restraints excluded: chain b2 residue 184 ILE Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 282 ARG Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 331 ASP Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 361 ILE Chi-restraints excluded: chain b2 residue 363 LEU Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 135 CYS Chi-restraints excluded: chain c2 residue 157 ILE Chi-restraints excluded: chain c2 residue 165 ASN Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain f2 residue 12 ASP Chi-restraints excluded: chain f2 residue 18 VAL Chi-restraints excluded: chain f2 residue 19 LEU Chi-restraints excluded: chain f2 residue 47 VAL Chi-restraints excluded: chain f2 residue 131 GLU Chi-restraints excluded: chain f2 residue 193 VAL Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain d2 residue 107 TRP Chi-restraints excluded: chain d2 residue 108 THR Chi-restraints excluded: chain q2 residue 18 LEU Chi-restraints excluded: chain q2 residue 19 SER Chi-restraints excluded: chain q2 residue 41 THR Chi-restraints excluded: chain q2 residue 46 LEU Chi-restraints excluded: chain q2 residue 60 THR Chi-restraints excluded: chain q2 residue 72 LYS Chi-restraints excluded: chain q2 residue 73 ASN Chi-restraints excluded: chain h2 residue 39 LEU Chi-restraints excluded: chain h2 residue 40 CYS Chi-restraints excluded: chain h2 residue 41 ASP Chi-restraints excluded: chain h2 residue 53 ASP Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain h2 residue 75 ASN Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Chi-restraints excluded: chain i2 residue 51 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 362 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 214 optimal weight: 6.9990 chunk 274 optimal weight: 0.5980 chunk 212 optimal weight: 6.9990 chunk 316 optimal weight: 5.9990 chunk 210 optimal weight: 0.0980 chunk 374 optimal weight: 0.8980 chunk 234 optimal weight: 7.9990 chunk 228 optimal weight: 0.8980 chunk 173 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a1 323 HIS a2 385 GLN c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f1 164 HIS q1 23 GLN a3 61 HIS ** a3 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 8 HIS ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32785 Z= 0.186 Angle : 0.674 14.463 44538 Z= 0.322 Chirality : 0.042 0.213 4837 Planarity : 0.004 0.061 5675 Dihedral : 10.667 153.429 4738 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 4.02 % Allowed : 18.92 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.14), residues: 3883 helix: 1.18 (0.12), residues: 2003 sheet: -0.57 (0.26), residues: 386 loop : -2.01 (0.16), residues: 1494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPb2 141 HIS 0.017 0.001 HISa1 323 PHE 0.032 0.001 PHEb1 276 TYR 0.020 0.001 TYRc1 164 ARG 0.008 0.000 ARGc1 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 595 time to evaluate : 3.586 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: a1 60 GLU cc_start: 0.8781 (tt0) cc_final: 0.8139 (tt0) REVERT: a1 115 ASP cc_start: 0.7524 (t0) cc_final: 0.7222 (t0) REVERT: a1 130 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7476 (mm-30) REVERT: a1 153 LEU cc_start: 0.9400 (tp) cc_final: 0.8994 (tt) REVERT: a1 194 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7235 (mtm180) REVERT: a1 219 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.5978 (tt) REVERT: a1 327 ASP cc_start: 0.8222 (t70) cc_final: 0.7956 (p0) REVERT: a1 329 MET cc_start: 0.8519 (mmm) cc_final: 0.8163 (tpt) REVERT: a1 376 CYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8289 (t) REVERT: a2 38 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8233 (tt) REVERT: a2 90 GLU cc_start: 0.8539 (mp0) cc_final: 0.8002 (mp0) REVERT: a2 99 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8559 (p) REVERT: a2 110 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7731 (tm-30) REVERT: b1 8 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7101 (t70) REVERT: b1 35 SER cc_start: 0.8949 (p) cc_final: 0.8419 (t) REVERT: b1 73 VAL cc_start: 0.9765 (t) cc_final: 0.9472 (p) REVERT: b1 96 MET cc_start: 0.7674 (mmm) cc_final: 0.7380 (mtt) REVERT: b1 121 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7344 (m-10) REVERT: b1 240 MET cc_start: 0.8423 (mmp) cc_final: 0.8031 (mmm) REVERT: b1 243 VAL cc_start: 0.8980 (m) cc_final: 0.8661 (m) REVERT: b1 282 ARG cc_start: 0.9118 (ttp-110) cc_final: 0.8582 (ttp-110) REVERT: c1 55 CYS cc_start: 0.8552 (p) cc_final: 0.8230 (p) REVERT: c1 109 LEU cc_start: 0.9038 (tp) cc_final: 0.8511 (pt) REVERT: c1 178 MET cc_start: 0.7555 (mmp) cc_final: 0.7053 (tpp) REVERT: c1 187 THR cc_start: 0.9397 (m) cc_final: 0.9061 (p) REVERT: c1 211 MET cc_start: 0.7413 (mmt) cc_final: 0.7105 (tmm) REVERT: c1 224 HIS cc_start: 0.8466 (OUTLIER) cc_final: 0.8177 (t-90) REVERT: f1 3 THR cc_start: 0.8792 (p) cc_final: 0.8463 (t) REVERT: f1 104 LYS cc_start: 0.8264 (mmmt) cc_final: 0.7445 (pttt) REVERT: d1 34 ASP cc_start: 0.8662 (p0) cc_final: 0.8443 (p0) REVERT: d1 73 GLN cc_start: 0.8035 (mm-40) cc_final: 0.7754 (mm-40) REVERT: q1 3 GLN cc_start: 0.8328 (pm20) cc_final: 0.7738 (pm20) REVERT: q1 47 ARG cc_start: 0.8608 (mtt180) cc_final: 0.7259 (mmt180) REVERT: h1 13 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.6952 (tm) REVERT: h1 38 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7877 (mt-10) REVERT: h1 42 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8141 (tp30) REVERT: i1 37 GLN cc_start: 0.8546 (mm-40) cc_final: 0.8321 (mp10) REVERT: a3 19 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7549 (mm) REVERT: a3 145 MET cc_start: 0.7881 (mtm) cc_final: 0.7660 (ttm) REVERT: a3 185 TYR cc_start: 0.8692 (t80) cc_final: 0.7977 (t80) REVERT: a3 223 TYR cc_start: 0.5268 (t80) cc_final: 0.4725 (p90) REVERT: a3 245 GLU cc_start: 0.8305 (tp30) cc_final: 0.7546 (tm-30) REVERT: a3 329 MET cc_start: 0.8684 (mmm) cc_final: 0.8304 (mmt) REVERT: a3 369 LEU cc_start: 0.8539 (mp) cc_final: 0.8000 (tt) REVERT: a3 375 VAL cc_start: 0.8991 (m) cc_final: 0.8701 (p) REVERT: a4 68 LEU cc_start: 0.9372 (tp) cc_final: 0.8980 (tp) REVERT: a4 158 HIS cc_start: 0.8455 (OUTLIER) cc_final: 0.7967 (t-90) REVERT: b2 12 LYS cc_start: 0.9006 (ttmt) cc_final: 0.8648 (ttmm) REVERT: b2 36 LEU cc_start: 0.8819 (mt) cc_final: 0.8569 (mt) REVERT: b2 43 LEU cc_start: 0.8562 (tt) cc_final: 0.8177 (mt) REVERT: b2 91 PHE cc_start: 0.8410 (m-80) cc_final: 0.8021 (m-80) REVERT: b2 129 MET cc_start: 0.8640 (mtm) cc_final: 0.8379 (mtp) REVERT: b2 240 MET cc_start: 0.8334 (mmp) cc_final: 0.7969 (mmt) REVERT: b2 263 ASN cc_start: 0.8156 (t0) cc_final: 0.7725 (t0) REVERT: b2 287 LYS cc_start: 0.8437 (mmtt) cc_final: 0.8035 (tttt) REVERT: b2 341 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8506 (mp10) REVERT: c2 114 SER cc_start: 0.9292 (m) cc_final: 0.9045 (t) REVERT: c2 203 MET cc_start: 0.8086 (mtm) cc_final: 0.7804 (mtm) REVERT: f2 17 GLU cc_start: 0.7918 (pm20) cc_final: 0.7261 (tp30) REVERT: f2 18 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7796 (t) REVERT: f2 69 LEU cc_start: 0.8860 (mm) cc_final: 0.8365 (tp) REVERT: f2 96 LEU cc_start: 0.6040 (tt) cc_final: 0.5589 (mp) REVERT: f2 153 PHE cc_start: 0.3989 (m-80) cc_final: 0.3406 (m-80) REVERT: f2 184 SER cc_start: 0.4950 (m) cc_final: 0.4712 (t) REVERT: q2 2 ARG cc_start: 0.7787 (mtp85) cc_final: 0.6943 (ptt180) REVERT: q2 3 GLN cc_start: 0.7890 (tt0) cc_final: 0.7639 (tt0) REVERT: q2 42 ARG cc_start: 0.7727 (tmt170) cc_final: 0.5315 (mtp85) REVERT: h2 59 PHE cc_start: 0.8830 (m-10) cc_final: 0.8456 (m-10) REVERT: h2 73 LEU cc_start: 0.8560 (tt) cc_final: 0.8256 (tp) REVERT: i2 50 LYS cc_start: 0.8644 (mptt) cc_final: 0.8429 (mptt) outliers start: 134 outliers final: 92 residues processed: 680 average time/residue: 0.4162 time to fit residues: 463.8697 Evaluate side-chains 666 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 561 time to evaluate : 3.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 4 TYR Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 161 THR Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 219 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 266 ASP Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 376 CYS Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 437 ILE Chi-restraints excluded: chain a2 residue 38 LEU Chi-restraints excluded: chain a2 residue 99 THR Chi-restraints excluded: chain a2 residue 100 SER Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 176 LEU Chi-restraints excluded: chain a2 residue 180 ASP Chi-restraints excluded: chain a2 residue 186 VAL Chi-restraints excluded: chain a2 residue 374 SER Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 12 LYS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 328 LEU Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 38 LEU Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain d1 residue 47 ILE Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 13 LEU Chi-restraints excluded: chain h1 residue 39 LEU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 55 THR Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 40 ASP Chi-restraints excluded: chain i1 residue 51 LEU Chi-restraints excluded: chain a3 residue 19 LEU Chi-restraints excluded: chain a3 residue 23 LEU Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 240 GLU Chi-restraints excluded: chain a3 residue 264 ASN Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a4 residue 20 HIS Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 158 HIS Chi-restraints excluded: chain a4 residue 160 ILE Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 364 LEU Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 42 ILE Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 171 ASP Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 331 ASP Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 135 CYS Chi-restraints excluded: chain c2 residue 165 ASN Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 200 ARG Chi-restraints excluded: chain f2 residue 18 VAL Chi-restraints excluded: chain f2 residue 19 LEU Chi-restraints excluded: chain f2 residue 131 GLU Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain d2 residue 107 TRP Chi-restraints excluded: chain q2 residue 18 LEU Chi-restraints excluded: chain q2 residue 73 ASN Chi-restraints excluded: chain h2 residue 39 LEU Chi-restraints excluded: chain h2 residue 40 CYS Chi-restraints excluded: chain h2 residue 53 ASP Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain h2 residue 75 ASN Chi-restraints excluded: chain i2 residue 12 LEU Chi-restraints excluded: chain i2 residue 48 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 231 optimal weight: 0.4980 chunk 149 optimal weight: 10.0000 chunk 223 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 73 optimal weight: 0.2980 chunk 72 optimal weight: 3.9990 chunk 238 optimal weight: 0.9990 chunk 255 optimal weight: 4.9990 chunk 185 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 294 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d1 79 GLN a3 173 ASN ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 8 HIS ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c2 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 32785 Z= 0.228 Angle : 0.692 15.111 44538 Z= 0.330 Chirality : 0.043 0.202 4837 Planarity : 0.004 0.078 5675 Dihedral : 10.534 152.974 4738 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.75 % Favored : 93.23 % Rotamer: Outliers : 4.17 % Allowed : 19.46 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3883 helix: 1.19 (0.12), residues: 2003 sheet: -0.43 (0.26), residues: 383 loop : -1.94 (0.16), residues: 1497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPa3 443 HIS 0.008 0.001 HISa1 252 PHE 0.031 0.001 PHEc2 152 TYR 0.020 0.001 TYRb2 358 ARG 0.007 0.000 ARGb1 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 569 time to evaluate : 3.605 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: a1 58 PHE cc_start: 0.9115 (OUTLIER) cc_final: 0.8816 (t80) REVERT: a1 60 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8180 (tt0) REVERT: a1 115 ASP cc_start: 0.7521 (t0) cc_final: 0.7214 (t0) REVERT: a1 130 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7473 (mm-30) REVERT: a1 153 LEU cc_start: 0.9426 (tp) cc_final: 0.9033 (tt) REVERT: a1 219 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6019 (tt) REVERT: a1 327 ASP cc_start: 0.8225 (t70) cc_final: 0.7944 (p0) REVERT: a1 329 MET cc_start: 0.8526 (mmm) cc_final: 0.8149 (tpt) REVERT: a1 376 CYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8286 (t) REVERT: a2 38 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8211 (tt) REVERT: a2 90 GLU cc_start: 0.8674 (mp0) cc_final: 0.8172 (mp0) REVERT: a2 99 THR cc_start: 0.8827 (OUTLIER) cc_final: 0.8585 (p) REVERT: b1 8 HIS cc_start: 0.7880 (OUTLIER) cc_final: 0.6974 (t70) REVERT: b1 35 SER cc_start: 0.9024 (p) cc_final: 0.8454 (t) REVERT: b1 73 VAL cc_start: 0.9760 (t) cc_final: 0.9476 (p) REVERT: b1 96 MET cc_start: 0.7723 (mmm) cc_final: 0.7405 (mtt) REVERT: b1 121 PHE cc_start: 0.7743 (OUTLIER) cc_final: 0.7510 (m-10) REVERT: b1 240 MET cc_start: 0.8456 (mmp) cc_final: 0.8052 (mmm) REVERT: b1 243 VAL cc_start: 0.9032 (m) cc_final: 0.8667 (m) REVERT: b1 282 ARG cc_start: 0.9101 (ttp-110) cc_final: 0.8634 (ttp-110) REVERT: b1 328 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8477 (tt) REVERT: c1 55 CYS cc_start: 0.8701 (p) cc_final: 0.8381 (p) REVERT: c1 109 LEU cc_start: 0.9059 (tp) cc_final: 0.8545 (pt) REVERT: c1 178 MET cc_start: 0.7632 (mmp) cc_final: 0.7158 (tpp) REVERT: c1 187 THR cc_start: 0.9397 (m) cc_final: 0.9068 (p) REVERT: c1 210 MET cc_start: 0.8021 (tpt) cc_final: 0.7606 (tpp) REVERT: c1 211 MET cc_start: 0.7413 (mmt) cc_final: 0.7088 (tmm) REVERT: c1 221 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.8447 (ppp) REVERT: c1 224 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8235 (t-90) REVERT: f1 3 THR cc_start: 0.8811 (p) cc_final: 0.8508 (t) REVERT: f1 104 LYS cc_start: 0.8269 (mmmt) cc_final: 0.7444 (pttt) REVERT: d1 34 ASP cc_start: 0.8688 (p0) cc_final: 0.8457 (p0) REVERT: q1 3 GLN cc_start: 0.8344 (pm20) cc_final: 0.7756 (pm20) REVERT: q1 22 GLU cc_start: 0.7982 (tp30) cc_final: 0.7561 (tp30) REVERT: q1 47 ARG cc_start: 0.8664 (mtt180) cc_final: 0.7209 (mmt180) REVERT: h1 13 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6937 (tm) REVERT: h1 38 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7951 (mt-10) REVERT: h1 42 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8116 (tp30) REVERT: i1 37 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8322 (mp10) REVERT: a3 19 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7451 (mm) REVERT: a3 50 GLU cc_start: 0.7850 (tp30) cc_final: 0.7625 (tp30) REVERT: a3 145 MET cc_start: 0.7916 (mtm) cc_final: 0.7586 (ttm) REVERT: a3 185 TYR cc_start: 0.8712 (t80) cc_final: 0.8196 (t80) REVERT: a3 245 GLU cc_start: 0.8316 (tp30) cc_final: 0.7481 (tm-30) REVERT: a3 329 MET cc_start: 0.8673 (mmm) cc_final: 0.8341 (mmt) REVERT: a3 369 LEU cc_start: 0.8565 (mp) cc_final: 0.8006 (tt) REVERT: a3 375 VAL cc_start: 0.9022 (m) cc_final: 0.8636 (p) REVERT: a4 68 LEU cc_start: 0.9421 (tp) cc_final: 0.9030 (tp) REVERT: b2 12 LYS cc_start: 0.9037 (ttmt) cc_final: 0.8658 (ttmm) REVERT: b2 36 LEU cc_start: 0.8864 (mt) cc_final: 0.8634 (mt) REVERT: b2 43 LEU cc_start: 0.8597 (tt) cc_final: 0.8169 (mt) REVERT: b2 91 PHE cc_start: 0.8415 (m-80) cc_final: 0.7684 (m-80) REVERT: b2 129 MET cc_start: 0.8672 (mtm) cc_final: 0.8396 (mtp) REVERT: b2 240 MET cc_start: 0.8270 (mmp) cc_final: 0.7814 (mmt) REVERT: b2 263 ASN cc_start: 0.8184 (t0) cc_final: 0.7756 (t0) REVERT: b2 287 LYS cc_start: 0.8471 (mmtt) cc_final: 0.7997 (tttt) REVERT: b2 316 MET cc_start: 0.7961 (ttm) cc_final: 0.7710 (tpp) REVERT: c2 114 SER cc_start: 0.9305 (m) cc_final: 0.9064 (t) REVERT: c2 203 MET cc_start: 0.8160 (mtm) cc_final: 0.7841 (mtm) REVERT: c2 215 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8830 (tp) REVERT: f2 17 GLU cc_start: 0.7948 (pm20) cc_final: 0.7210 (tp30) REVERT: f2 18 VAL cc_start: 0.8098 (OUTLIER) cc_final: 0.7827 (t) REVERT: f2 69 LEU cc_start: 0.8861 (mm) cc_final: 0.8399 (tp) REVERT: f2 96 LEU cc_start: 0.5784 (tt) cc_final: 0.5355 (mp) REVERT: f2 153 PHE cc_start: 0.4276 (m-80) cc_final: 0.3441 (m-80) REVERT: f2 184 SER cc_start: 0.4960 (m) cc_final: 0.4736 (t) REVERT: q2 2 ARG cc_start: 0.7875 (mtp85) cc_final: 0.6940 (ptt180) REVERT: q2 3 GLN cc_start: 0.8015 (tt0) cc_final: 0.7759 (tt0) REVERT: q2 9 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.7373 (mtp85) REVERT: q2 42 ARG cc_start: 0.7752 (tmt170) cc_final: 0.5376 (mtp85) REVERT: h2 52 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7872 (tm-30) REVERT: h2 55 THR cc_start: 0.7207 (m) cc_final: 0.6416 (p) REVERT: h2 59 PHE cc_start: 0.8834 (m-10) cc_final: 0.8507 (m-10) REVERT: h2 73 LEU cc_start: 0.8578 (tt) cc_final: 0.8303 (tp) REVERT: i2 32 GLU cc_start: 0.8598 (tt0) cc_final: 0.8288 (tt0) REVERT: i2 50 LYS cc_start: 0.8673 (mptt) cc_final: 0.8444 (mptt) outliers start: 139 outliers final: 101 residues processed: 653 average time/residue: 0.3987 time to fit residues: 428.8537 Evaluate side-chains 669 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 552 time to evaluate : 3.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 4 TYR Chi-restraints excluded: chain a1 residue 58 PHE Chi-restraints excluded: chain a1 residue 60 GLU Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 161 THR Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 219 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 266 ASP Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 376 CYS Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 437 ILE Chi-restraints excluded: chain a1 residue 443 TRP Chi-restraints excluded: chain a2 residue 38 LEU Chi-restraints excluded: chain a2 residue 99 THR Chi-restraints excluded: chain a2 residue 100 SER Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 176 LEU Chi-restraints excluded: chain a2 residue 180 ASP Chi-restraints excluded: chain a2 residue 186 VAL Chi-restraints excluded: chain a2 residue 276 GLN Chi-restraints excluded: chain a2 residue 374 SER Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 12 LYS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 78 ILE Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 184 ILE Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 328 LEU Chi-restraints excluded: chain b1 residue 353 LEU Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 97 ASN Chi-restraints excluded: chain c1 residue 124 GLU Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 221 MET Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 38 LEU Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 13 LEU Chi-restraints excluded: chain h1 residue 39 LEU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 55 THR Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 40 ASP Chi-restraints excluded: chain i1 residue 51 LEU Chi-restraints excluded: chain a3 residue 19 LEU Chi-restraints excluded: chain a3 residue 23 LEU Chi-restraints excluded: chain a3 residue 100 LYS Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 240 GLU Chi-restraints excluded: chain a3 residue 264 ASN Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 320 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a4 residue 20 HIS Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 126 VAL Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain a4 residue 397 THR Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 42 ILE Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 92 ILE Chi-restraints excluded: chain b2 residue 171 ASP Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 331 ASP Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 135 CYS Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain c2 residue 215 LEU Chi-restraints excluded: chain f2 residue 18 VAL Chi-restraints excluded: chain f2 residue 19 LEU Chi-restraints excluded: chain f2 residue 78 LEU Chi-restraints excluded: chain d2 residue 45 GLU Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain d2 residue 107 TRP Chi-restraints excluded: chain d2 residue 108 THR Chi-restraints excluded: chain q2 residue 18 LEU Chi-restraints excluded: chain q2 residue 34 ILE Chi-restraints excluded: chain q2 residue 73 ASN Chi-restraints excluded: chain h2 residue 39 LEU Chi-restraints excluded: chain h2 residue 53 ASP Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain h2 residue 75 ASN Chi-restraints excluded: chain i2 residue 12 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 341 optimal weight: 6.9990 chunk 359 optimal weight: 3.9990 chunk 327 optimal weight: 3.9990 chunk 349 optimal weight: 4.9990 chunk 210 optimal weight: 0.9990 chunk 152 optimal weight: 6.9990 chunk 274 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 315 optimal weight: 0.8980 chunk 330 optimal weight: 7.9990 chunk 348 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d1 79 GLN q1 23 GLN ** h1 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 8 HIS ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 32785 Z= 0.284 Angle : 0.720 15.278 44538 Z= 0.345 Chirality : 0.044 0.193 4837 Planarity : 0.005 0.078 5675 Dihedral : 10.564 153.301 4738 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 4.20 % Allowed : 19.61 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.14), residues: 3883 helix: 1.18 (0.12), residues: 1997 sheet: -0.42 (0.26), residues: 383 loop : -1.90 (0.17), residues: 1503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPa3 443 HIS 0.008 0.001 HISb1 196 PHE 0.029 0.002 PHEa4 435 TYR 0.041 0.002 TYRc1 164 ARG 0.006 0.001 ARGb1 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 555 time to evaluate : 3.904 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: a1 58 PHE cc_start: 0.9162 (OUTLIER) cc_final: 0.8909 (t80) REVERT: a1 60 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8286 (tt0) REVERT: a1 115 ASP cc_start: 0.7537 (t0) cc_final: 0.7242 (t0) REVERT: a1 130 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7494 (mm-30) REVERT: a1 327 ASP cc_start: 0.8250 (t70) cc_final: 0.8017 (p0) REVERT: a1 329 MET cc_start: 0.8541 (mmm) cc_final: 0.8150 (tpt) REVERT: a1 376 CYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8258 (t) REVERT: a2 90 GLU cc_start: 0.8802 (mp0) cc_final: 0.8276 (mp0) REVERT: a2 99 THR cc_start: 0.8845 (OUTLIER) cc_final: 0.8606 (p) REVERT: b1 8 HIS cc_start: 0.7872 (OUTLIER) cc_final: 0.7196 (t70) REVERT: b1 35 SER cc_start: 0.9082 (p) cc_final: 0.8547 (t) REVERT: b1 121 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7533 (m-10) REVERT: b1 240 MET cc_start: 0.8511 (mmp) cc_final: 0.7836 (mmm) REVERT: b1 243 VAL cc_start: 0.9042 (m) cc_final: 0.8696 (m) REVERT: b1 282 ARG cc_start: 0.9090 (ttp-110) cc_final: 0.8224 (ttp80) REVERT: b1 328 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8444 (tt) REVERT: c1 55 CYS cc_start: 0.8726 (p) cc_final: 0.8409 (p) REVERT: c1 109 LEU cc_start: 0.9101 (tp) cc_final: 0.8621 (pt) REVERT: c1 187 THR cc_start: 0.9407 (m) cc_final: 0.9067 (p) REVERT: c1 210 MET cc_start: 0.7941 (tpt) cc_final: 0.7736 (tpp) REVERT: c1 221 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8483 (ppp) REVERT: c1 224 HIS cc_start: 0.8529 (OUTLIER) cc_final: 0.8316 (t-90) REVERT: f1 3 THR cc_start: 0.8779 (p) cc_final: 0.8503 (t) REVERT: f1 104 LYS cc_start: 0.8278 (mmmt) cc_final: 0.7461 (ptmt) REVERT: d1 34 ASP cc_start: 0.8742 (p0) cc_final: 0.8479 (p0) REVERT: q1 3 GLN cc_start: 0.8375 (pm20) cc_final: 0.7791 (pm20) REVERT: q1 22 GLU cc_start: 0.7915 (tp30) cc_final: 0.7533 (tp30) REVERT: q1 47 ARG cc_start: 0.8664 (mtt180) cc_final: 0.7309 (mmt180) REVERT: h1 13 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.6956 (tm) REVERT: h1 38 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7989 (mt-10) REVERT: h1 42 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: a3 19 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7443 (mm) REVERT: a3 145 MET cc_start: 0.7945 (mtm) cc_final: 0.7364 (ttm) REVERT: a3 185 TYR cc_start: 0.8746 (t80) cc_final: 0.8119 (t80) REVERT: a3 245 GLU cc_start: 0.8321 (tp30) cc_final: 0.7494 (tm-30) REVERT: a3 329 MET cc_start: 0.8668 (mmm) cc_final: 0.8355 (mmt) REVERT: a3 369 LEU cc_start: 0.8572 (mp) cc_final: 0.7998 (tt) REVERT: a4 68 LEU cc_start: 0.9462 (tp) cc_final: 0.9074 (tp) REVERT: b2 12 LYS cc_start: 0.9043 (ttmt) cc_final: 0.8652 (ttmm) REVERT: b2 36 LEU cc_start: 0.8904 (mt) cc_final: 0.8680 (mt) REVERT: b2 43 LEU cc_start: 0.8579 (tt) cc_final: 0.8137 (mt) REVERT: b2 129 MET cc_start: 0.8719 (mtm) cc_final: 0.8450 (mtp) REVERT: b2 240 MET cc_start: 0.8300 (mmp) cc_final: 0.7845 (mmt) REVERT: b2 263 ASN cc_start: 0.8186 (t0) cc_final: 0.7785 (t0) REVERT: b2 287 LYS cc_start: 0.8482 (mmtt) cc_final: 0.7976 (tttt) REVERT: b2 313 ARG cc_start: 0.8014 (ptm-80) cc_final: 0.7736 (ttp-170) REVERT: c2 114 SER cc_start: 0.9313 (m) cc_final: 0.9101 (t) REVERT: f2 17 GLU cc_start: 0.7955 (pm20) cc_final: 0.7207 (tp30) REVERT: f2 18 VAL cc_start: 0.8311 (OUTLIER) cc_final: 0.8007 (t) REVERT: f2 69 LEU cc_start: 0.8883 (mm) cc_final: 0.8404 (tp) REVERT: f2 96 LEU cc_start: 0.5886 (tt) cc_final: 0.5459 (mp) REVERT: f2 184 SER cc_start: 0.4965 (m) cc_final: 0.4746 (t) REVERT: q2 2 ARG cc_start: 0.7914 (mtp85) cc_final: 0.6945 (ptt180) REVERT: q2 9 ARG cc_start: 0.8390 (mmm-85) cc_final: 0.7418 (mtp85) REVERT: q2 42 ARG cc_start: 0.7700 (tmt170) cc_final: 0.5330 (mtp85) REVERT: h2 28 GLU cc_start: 0.7479 (tp30) cc_final: 0.7212 (tp30) REVERT: h2 52 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7810 (tm-30) REVERT: h2 59 PHE cc_start: 0.8813 (m-10) cc_final: 0.8483 (m-10) REVERT: i2 14 PHE cc_start: 0.8691 (m-10) cc_final: 0.8471 (m-10) REVERT: i2 50 LYS cc_start: 0.8701 (mptt) cc_final: 0.8462 (mptt) outliers start: 140 outliers final: 107 residues processed: 640 average time/residue: 0.3994 time to fit residues: 423.2619 Evaluate side-chains 666 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 546 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 4 TYR Chi-restraints excluded: chain a1 residue 58 PHE Chi-restraints excluded: chain a1 residue 60 GLU Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 161 THR Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 219 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 266 ASP Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 376 CYS Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 437 ILE Chi-restraints excluded: chain a1 residue 443 TRP Chi-restraints excluded: chain a2 residue 99 THR Chi-restraints excluded: chain a2 residue 100 SER Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 176 LEU Chi-restraints excluded: chain a2 residue 180 ASP Chi-restraints excluded: chain a2 residue 186 VAL Chi-restraints excluded: chain a2 residue 276 GLN Chi-restraints excluded: chain a2 residue 374 SER Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 12 LYS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 78 ILE Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 328 LEU Chi-restraints excluded: chain b1 residue 353 LEU Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 97 ASN Chi-restraints excluded: chain c1 residue 131 LEU Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 177 THR Chi-restraints excluded: chain c1 residue 207 MET Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 221 MET Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain f1 residue 147 ILE Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 13 LEU Chi-restraints excluded: chain h1 residue 27 LEU Chi-restraints excluded: chain h1 residue 39 LEU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 40 ASP Chi-restraints excluded: chain a3 residue 19 LEU Chi-restraints excluded: chain a3 residue 23 LEU Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 240 GLU Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 320 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a4 residue 20 HIS Chi-restraints excluded: chain a4 residue 51 ILE Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 116 VAL Chi-restraints excluded: chain a4 residue 126 VAL Chi-restraints excluded: chain a4 residue 175 SER Chi-restraints excluded: chain a4 residue 186 VAL Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain a4 residue 397 THR Chi-restraints excluded: chain b2 residue 28 SER Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 42 ILE Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 171 ASP Chi-restraints excluded: chain b2 residue 184 ILE Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 331 ASP Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 135 CYS Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain f2 residue 12 ASP Chi-restraints excluded: chain f2 residue 18 VAL Chi-restraints excluded: chain f2 residue 19 LEU Chi-restraints excluded: chain f2 residue 78 LEU Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain d2 residue 107 TRP Chi-restraints excluded: chain d2 residue 108 THR Chi-restraints excluded: chain q2 residue 18 LEU Chi-restraints excluded: chain q2 residue 46 LEU Chi-restraints excluded: chain q2 residue 60 THR Chi-restraints excluded: chain q2 residue 73 ASN Chi-restraints excluded: chain h2 residue 39 LEU Chi-restraints excluded: chain h2 residue 41 ASP Chi-restraints excluded: chain h2 residue 53 ASP Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain h2 residue 75 ASN Chi-restraints excluded: chain i2 residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 229 optimal weight: 1.9990 chunk 369 optimal weight: 0.5980 chunk 225 optimal weight: 0.9990 chunk 175 optimal weight: 2.9990 chunk 256 optimal weight: 4.9990 chunk 387 optimal weight: 0.9980 chunk 356 optimal weight: 1.9990 chunk 308 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 238 optimal weight: 6.9990 chunk 189 optimal weight: 9.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c1 75 ASN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d1 79 GLN q1 23 GLN ** h1 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 8 HIS ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.4552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 32785 Z= 0.228 Angle : 0.691 14.887 44538 Z= 0.330 Chirality : 0.043 0.203 4837 Planarity : 0.004 0.080 5675 Dihedral : 10.410 153.031 4738 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 3.93 % Allowed : 20.03 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3883 helix: 1.21 (0.12), residues: 2009 sheet: -0.38 (0.27), residues: 375 loop : -1.90 (0.17), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPa3 443 HIS 0.007 0.001 HISa1 252 PHE 0.028 0.001 PHEb1 276 TYR 0.049 0.001 TYRb2 273 ARG 0.006 0.000 ARGb1 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7766 Ramachandran restraints generated. 3883 Oldfield, 0 Emsley, 3883 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 560 time to evaluate : 3.687 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: a1 58 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8730 (t80) REVERT: a1 60 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.7858 (tm-30) REVERT: a1 115 ASP cc_start: 0.7550 (t0) cc_final: 0.7251 (t0) REVERT: a1 130 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7463 (mm-30) REVERT: a1 153 LEU cc_start: 0.9424 (tp) cc_final: 0.9022 (tt) REVERT: a1 219 LEU cc_start: 0.6502 (OUTLIER) cc_final: 0.6053 (tt) REVERT: a1 327 ASP cc_start: 0.8191 (t70) cc_final: 0.7976 (p0) REVERT: a1 329 MET cc_start: 0.8521 (mmm) cc_final: 0.8159 (tpt) REVERT: a1 376 CYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8270 (t) REVERT: a2 90 GLU cc_start: 0.8829 (mp0) cc_final: 0.8260 (mp0) REVERT: a2 99 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8579 (p) REVERT: b1 8 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.6932 (t70) REVERT: b1 35 SER cc_start: 0.9101 (p) cc_final: 0.8554 (t) REVERT: b1 73 VAL cc_start: 0.9735 (t) cc_final: 0.9459 (p) REVERT: b1 96 MET cc_start: 0.7664 (mmm) cc_final: 0.7239 (mtt) REVERT: b1 121 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7519 (m-10) REVERT: b1 240 MET cc_start: 0.8467 (mmp) cc_final: 0.7783 (mmm) REVERT: b1 243 VAL cc_start: 0.9016 (m) cc_final: 0.8645 (m) REVERT: b1 282 ARG cc_start: 0.9058 (ttp-110) cc_final: 0.8610 (ttp-110) REVERT: b1 328 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8423 (tt) REVERT: c1 55 CYS cc_start: 0.8664 (p) cc_final: 0.8375 (p) REVERT: c1 109 LEU cc_start: 0.9018 (tp) cc_final: 0.8670 (pt) REVERT: c1 187 THR cc_start: 0.9401 (m) cc_final: 0.9070 (p) REVERT: c1 221 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8487 (ppp) REVERT: c1 224 HIS cc_start: 0.8552 (OUTLIER) cc_final: 0.8280 (t-90) REVERT: f1 3 THR cc_start: 0.8827 (p) cc_final: 0.8543 (t) REVERT: f1 87 MET cc_start: 0.4735 (tpt) cc_final: 0.3815 (ttt) REVERT: f1 104 LYS cc_start: 0.8293 (mmmt) cc_final: 0.7465 (ptmt) REVERT: d1 34 ASP cc_start: 0.8733 (p0) cc_final: 0.8472 (p0) REVERT: d1 73 GLN cc_start: 0.8114 (mm-40) cc_final: 0.7860 (mm-40) REVERT: q1 3 GLN cc_start: 0.8340 (pm20) cc_final: 0.7758 (pm20) REVERT: q1 22 GLU cc_start: 0.7960 (tp30) cc_final: 0.7547 (tp30) REVERT: q1 47 ARG cc_start: 0.8655 (mtt180) cc_final: 0.7247 (mmt180) REVERT: h1 13 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.6934 (tm) REVERT: h1 42 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8119 (tp30) REVERT: a3 19 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7398 (mm) REVERT: a3 145 MET cc_start: 0.7869 (mtm) cc_final: 0.7444 (ttm) REVERT: a3 185 TYR cc_start: 0.8687 (t80) cc_final: 0.8011 (t80) REVERT: a3 245 GLU cc_start: 0.8300 (tp30) cc_final: 0.7454 (tm-30) REVERT: a3 329 MET cc_start: 0.8661 (mmm) cc_final: 0.8214 (tpp) REVERT: a3 369 LEU cc_start: 0.8518 (mp) cc_final: 0.7971 (tt) REVERT: a4 68 LEU cc_start: 0.9427 (tp) cc_final: 0.9041 (tp) REVERT: a4 105 MET cc_start: 0.8789 (ttt) cc_final: 0.8528 (ttm) REVERT: b2 12 LYS cc_start: 0.9031 (ttmt) cc_final: 0.8622 (ttmm) REVERT: b2 36 LEU cc_start: 0.8852 (mt) cc_final: 0.8634 (mt) REVERT: b2 43 LEU cc_start: 0.8616 (tt) cc_final: 0.8191 (mt) REVERT: b2 240 MET cc_start: 0.8273 (mmp) cc_final: 0.7777 (mmt) REVERT: b2 252 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7397 (p0) REVERT: b2 263 ASN cc_start: 0.8078 (t0) cc_final: 0.7644 (t0) REVERT: b2 287 LYS cc_start: 0.8481 (mmtt) cc_final: 0.7886 (tttt) REVERT: b2 313 ARG cc_start: 0.7980 (ptm-80) cc_final: 0.7597 (ttp-170) REVERT: c2 114 SER cc_start: 0.9307 (m) cc_final: 0.9085 (t) REVERT: f2 17 GLU cc_start: 0.7899 (pm20) cc_final: 0.7266 (tp30) REVERT: f2 18 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.8001 (t) REVERT: f2 69 LEU cc_start: 0.8863 (mm) cc_final: 0.8386 (tp) REVERT: f2 96 LEU cc_start: 0.5857 (tt) cc_final: 0.5509 (mt) REVERT: f2 184 SER cc_start: 0.4979 (m) cc_final: 0.4744 (t) REVERT: q2 2 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7016 (ptt180) REVERT: q2 9 ARG cc_start: 0.8382 (mmm-85) cc_final: 0.7405 (mtp85) REVERT: q2 42 ARG cc_start: 0.7648 (tmt170) cc_final: 0.5295 (mtp85) REVERT: h2 52 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7841 (tm-30) REVERT: h2 59 PHE cc_start: 0.8821 (m-10) cc_final: 0.8506 (m-10) REVERT: i2 48 GLU cc_start: 0.7944 (mm-30) cc_final: 0.7416 (mp0) REVERT: i2 50 LYS cc_start: 0.8668 (mptt) cc_final: 0.8453 (mptt) outliers start: 131 outliers final: 104 residues processed: 643 average time/residue: 0.3979 time to fit residues: 424.4505 Evaluate side-chains 662 residues out of total 3330 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 543 time to evaluate : 3.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a1 residue 4 TYR Chi-restraints excluded: chain a1 residue 58 PHE Chi-restraints excluded: chain a1 residue 60 GLU Chi-restraints excluded: chain a1 residue 61 HIS Chi-restraints excluded: chain a1 residue 62 LEU Chi-restraints excluded: chain a1 residue 149 VAL Chi-restraints excluded: chain a1 residue 161 THR Chi-restraints excluded: chain a1 residue 174 VAL Chi-restraints excluded: chain a1 residue 186 LEU Chi-restraints excluded: chain a1 residue 195 MET Chi-restraints excluded: chain a1 residue 219 LEU Chi-restraints excluded: chain a1 residue 230 THR Chi-restraints excluded: chain a1 residue 258 GLU Chi-restraints excluded: chain a1 residue 266 ASP Chi-restraints excluded: chain a1 residue 345 LEU Chi-restraints excluded: chain a1 residue 363 ASN Chi-restraints excluded: chain a1 residue 368 HIS Chi-restraints excluded: chain a1 residue 376 CYS Chi-restraints excluded: chain a1 residue 379 ILE Chi-restraints excluded: chain a1 residue 437 ILE Chi-restraints excluded: chain a1 residue 443 TRP Chi-restraints excluded: chain a2 residue 99 THR Chi-restraints excluded: chain a2 residue 100 SER Chi-restraints excluded: chain a2 residue 109 VAL Chi-restraints excluded: chain a2 residue 110 GLU Chi-restraints excluded: chain a2 residue 137 VAL Chi-restraints excluded: chain a2 residue 176 LEU Chi-restraints excluded: chain a2 residue 180 ASP Chi-restraints excluded: chain a2 residue 186 VAL Chi-restraints excluded: chain a2 residue 276 GLN Chi-restraints excluded: chain a2 residue 374 SER Chi-restraints excluded: chain b1 residue 8 HIS Chi-restraints excluded: chain b1 residue 12 LYS Chi-restraints excluded: chain b1 residue 37 LEU Chi-restraints excluded: chain b1 residue 51 LEU Chi-restraints excluded: chain b1 residue 78 ILE Chi-restraints excluded: chain b1 residue 121 PHE Chi-restraints excluded: chain b1 residue 215 THR Chi-restraints excluded: chain b1 residue 237 LEU Chi-restraints excluded: chain b1 residue 302 VAL Chi-restraints excluded: chain b1 residue 328 LEU Chi-restraints excluded: chain b1 residue 360 LEU Chi-restraints excluded: chain c1 residue 42 SER Chi-restraints excluded: chain c1 residue 54 VAL Chi-restraints excluded: chain c1 residue 97 ASN Chi-restraints excluded: chain c1 residue 131 LEU Chi-restraints excluded: chain c1 residue 142 LEU Chi-restraints excluded: chain c1 residue 177 THR Chi-restraints excluded: chain c1 residue 207 MET Chi-restraints excluded: chain c1 residue 208 LEU Chi-restraints excluded: chain c1 residue 215 LEU Chi-restraints excluded: chain c1 residue 221 MET Chi-restraints excluded: chain c1 residue 224 HIS Chi-restraints excluded: chain f1 residue 5 ILE Chi-restraints excluded: chain f1 residue 61 SER Chi-restraints excluded: chain f1 residue 147 ILE Chi-restraints excluded: chain q1 residue 12 HIS Chi-restraints excluded: chain q1 residue 18 LEU Chi-restraints excluded: chain q1 residue 44 CYS Chi-restraints excluded: chain h1 residue 13 LEU Chi-restraints excluded: chain h1 residue 39 LEU Chi-restraints excluded: chain h1 residue 42 GLU Chi-restraints excluded: chain h1 residue 76 SER Chi-restraints excluded: chain h1 residue 77 LEU Chi-restraints excluded: chain i1 residue 17 THR Chi-restraints excluded: chain i1 residue 40 ASP Chi-restraints excluded: chain a3 residue 19 LEU Chi-restraints excluded: chain a3 residue 23 LEU Chi-restraints excluded: chain a3 residue 161 THR Chi-restraints excluded: chain a3 residue 174 VAL Chi-restraints excluded: chain a3 residue 228 VAL Chi-restraints excluded: chain a3 residue 240 GLU Chi-restraints excluded: chain a3 residue 276 ILE Chi-restraints excluded: chain a3 residue 290 LEU Chi-restraints excluded: chain a3 residue 320 LEU Chi-restraints excluded: chain a3 residue 345 LEU Chi-restraints excluded: chain a3 residue 350 THR Chi-restraints excluded: chain a4 residue 20 HIS Chi-restraints excluded: chain a4 residue 51 ILE Chi-restraints excluded: chain a4 residue 99 THR Chi-restraints excluded: chain a4 residue 109 VAL Chi-restraints excluded: chain a4 residue 116 VAL Chi-restraints excluded: chain a4 residue 126 VAL Chi-restraints excluded: chain a4 residue 186 VAL Chi-restraints excluded: chain a4 residue 193 ASP Chi-restraints excluded: chain a4 residue 370 MET Chi-restraints excluded: chain a4 residue 397 THR Chi-restraints excluded: chain b2 residue 37 LEU Chi-restraints excluded: chain b2 residue 42 ILE Chi-restraints excluded: chain b2 residue 67 THR Chi-restraints excluded: chain b2 residue 78 ILE Chi-restraints excluded: chain b2 residue 171 ASP Chi-restraints excluded: chain b2 residue 184 ILE Chi-restraints excluded: chain b2 residue 233 ILE Chi-restraints excluded: chain b2 residue 243 VAL Chi-restraints excluded: chain b2 residue 252 ASP Chi-restraints excluded: chain b2 residue 300 VAL Chi-restraints excluded: chain b2 residue 331 ASP Chi-restraints excluded: chain b2 residue 359 PHE Chi-restraints excluded: chain b2 residue 371 ILE Chi-restraints excluded: chain c2 residue 80 MET Chi-restraints excluded: chain c2 residue 135 CYS Chi-restraints excluded: chain c2 residue 179 SER Chi-restraints excluded: chain c2 residue 183 LYS Chi-restraints excluded: chain c2 residue 198 ASP Chi-restraints excluded: chain f2 residue 12 ASP Chi-restraints excluded: chain f2 residue 18 VAL Chi-restraints excluded: chain f2 residue 19 LEU Chi-restraints excluded: chain f2 residue 78 LEU Chi-restraints excluded: chain d2 residue 54 LEU Chi-restraints excluded: chain d2 residue 107 TRP Chi-restraints excluded: chain q2 residue 18 LEU Chi-restraints excluded: chain q2 residue 46 LEU Chi-restraints excluded: chain q2 residue 73 ASN Chi-restraints excluded: chain h2 residue 41 ASP Chi-restraints excluded: chain h2 residue 61 PHE Chi-restraints excluded: chain h2 residue 62 LEU Chi-restraints excluded: chain h2 residue 75 ASN Chi-restraints excluded: chain i2 residue 12 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 389 random chunks: chunk 245 optimal weight: 7.9990 chunk 328 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 284 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 85 optimal weight: 6.9990 chunk 309 optimal weight: 0.9990 chunk 129 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a1 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a2 143 GLN ** f1 2 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d1 79 GLN ** h1 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a3 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 8 HIS ** b2 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b2 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.121475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.102775 restraints weight = 68974.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.105552 restraints weight = 38041.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.107439 restraints weight = 25445.833| |-----------------------------------------------------------------------------| r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 32785 Z= 0.208 Angle : 0.693 14.346 44538 Z= 0.331 Chirality : 0.042 0.210 4837 Planarity : 0.004 0.075 5675 Dihedral : 10.299 151.845 4738 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 3.90 % Allowed : 20.18 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3883 helix: 1.28 (0.12), residues: 2004 sheet: -0.33 (0.26), residues: 380 loop : -1.83 (0.17), residues: 1499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPa3 443 HIS 0.007 0.001 HISa1 252 PHE 0.028 0.001 PHEb1 276 TYR 0.049 0.001 TYRc1 164 ARG 0.006 0.000 ARGb1 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8229.56 seconds wall clock time: 149 minutes 1.93 seconds (8941.93 seconds total)