Starting phenix.real_space_refine on Wed Feb 14 07:14:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezh_31387/02_2024/7ezh_31387_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezh_31387/02_2024/7ezh_31387.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezh_31387/02_2024/7ezh_31387.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezh_31387/02_2024/7ezh_31387.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezh_31387/02_2024/7ezh_31387_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ezh_31387/02_2024/7ezh_31387_updated.pdb" } resolution = 3.2 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= 0.003 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 72 5.16 5 C 5643 2.51 5 N 1489 2.21 5 O 1634 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A ARG 208": "NH1" <-> "NH2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 313": "NH1" <-> "NH2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D ARG 150": "NH1" <-> "NH2" Residue "D ARG 197": "NH1" <-> "NH2" Residue "D ARG 345": "NH1" <-> "NH2" Residue "D ARG 376": "NH1" <-> "NH2" Residue "H ARG 18": "NH1" <-> "NH2" Residue "H TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 202": "NH1" <-> "NH2" Residue "H GLU 220": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8838 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "B" Number of atoms: 2561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2561 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "D" Number of atoms: 2306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2306 Classifications: {'peptide': 296} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 12, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 39 Chain: "G" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 404 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1736 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 222} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 32 Chain: "P" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.97, per 1000 atoms: 0.56 Number of scatterers: 8838 At special positions: 0 Unit cell: (106.59, 112.86, 119.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 72 16.00 O 1634 8.00 N 1489 7.00 C 5643 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 149 " distance=2.04 Simple disulfide: pdb=" SG CYS D 114 " - pdb=" SG CYS D 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 1.7 seconds 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 33 helices and 13 sheets defined 36.6% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 9 through 32 Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.607A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 3.634A pdb=" N TYR A 230 " --> pdb=" O LEU A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 278 Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.558A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 Processing helix chain 'B' and resid 4 through 25 removed outlier: 5.355A pdb=" N GLN B 9 " --> pdb=" O ASP B 5 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.545A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 68 Processing helix chain 'D' and resid 70 through 72 No H-bonds generated for 'chain 'D' and resid 70 through 72' Processing helix chain 'D' and resid 75 through 104 Proline residue: D 96 - end of helix Proline residue: D 101 - end of helix Processing helix chain 'D' and resid 111 through 144 Processing helix chain 'D' and resid 146 through 152 removed outlier: 3.589A pdb=" N ARG D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL D 151 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP D 152 " --> pdb=" O GLN D 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 146 through 152' Processing helix chain 'D' and resid 155 through 179 removed outlier: 3.536A pdb=" N THR D 174 " --> pdb=" O PHE D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 203 through 217 Processing helix chain 'D' and resid 219 through 244 removed outlier: 3.693A pdb=" N GLY D 239 " --> pdb=" O GLU D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 338 removed outlier: 3.508A pdb=" N LYS D 308 " --> pdb=" O ASN D 304 " (cutoff:3.500A) Proline residue: D 328 - end of helix Processing helix chain 'D' and resid 340 through 347 Processing helix chain 'D' and resid 350 through 369 removed outlier: 3.719A pdb=" N SER D 362 " --> pdb=" O LEU D 358 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER D 363 " --> pdb=" O SER D 359 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS D 364 " --> pdb=" O TYR D 360 " (cutoff:3.500A) Proline residue: D 367 - end of helix Processing helix chain 'D' and resid 371 through 373 No H-bonds generated for 'chain 'D' and resid 371 through 373' Processing helix chain 'D' and resid 375 through 383 removed outlier: 4.364A pdb=" N MET D 382 " --> pdb=" O ARG D 378 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 23 removed outlier: 3.662A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'H' and resid 29 through 31 No H-bonds generated for 'chain 'H' and resid 29 through 31' Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'H' and resid 221 through 223 No H-bonds generated for 'chain 'H' and resid 221 through 223' Processing sheet with id= A, first strand: chain 'A' and resid 263 through 269 removed outlier: 3.650A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.826A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.867A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 139 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.499A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.749A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 231 through 234 removed outlier: 3.771A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.461A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.708A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 180 through 187 removed outlier: 3.609A pdb=" N ARG D 197 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 191 " --> pdb=" O LYS D 187 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'H' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.561A pdb=" N ALA H 92 " --> pdb=" O LEU H 117 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'H' and resid 140 through 142 removed outlier: 3.730A pdb=" N CYS H 159 " --> pdb=" O PHE H 212 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE H 212 " --> pdb=" O CYS H 159 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'H' and resid 146 through 148 removed outlier: 6.081A pdb=" N LYS H 244 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLY H 225 " --> pdb=" O LEU H 245 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 3.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2822 1.35 - 1.47: 2251 1.47 - 1.59: 3841 1.59 - 1.71: 1 1.71 - 1.83: 107 Bond restraints: 9022 Sorted by residual: bond pdb=" O1 TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.462 1.635 -0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.537 0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" N VAL H 119 " pdb=" CA VAL H 119 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.15e-02 7.56e+03 1.42e+01 bond pdb=" N SER H 120 " pdb=" CA SER H 120 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.13e+00 bond pdb=" N ASP A 350 " pdb=" CA ASP A 350 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.46e+00 ... (remaining 9017 not shown) Histogram of bond angle deviations from ideal: 100.16 - 106.94: 217 106.94 - 113.72: 4987 113.72 - 120.50: 3497 120.50 - 127.28: 3448 127.28 - 134.06: 89 Bond angle restraints: 12238 Sorted by residual: angle pdb=" N SER A 326 " pdb=" CA SER A 326 " pdb=" C SER A 326 " ideal model delta sigma weight residual 111.14 104.94 6.20 1.08e+00 8.57e-01 3.30e+01 angle pdb=" C GLN D 153 " pdb=" CA GLN D 153 " pdb=" CB GLN D 153 " ideal model delta sigma weight residual 111.88 104.45 7.43 1.41e+00 5.03e-01 2.77e+01 angle pdb=" C THR A 329 " pdb=" CA THR A 329 " pdb=" CB THR A 329 " ideal model delta sigma weight residual 110.42 118.59 -8.17 1.99e+00 2.53e-01 1.69e+01 angle pdb=" CA ALA H 136 " pdb=" C ALA H 136 " pdb=" O ALA H 136 " ideal model delta sigma weight residual 121.54 117.25 4.29 1.16e+00 7.43e-01 1.37e+01 angle pdb=" N GLY B 141 " pdb=" CA GLY B 141 " pdb=" C GLY B 141 " ideal model delta sigma weight residual 113.18 121.71 -8.53 2.37e+00 1.78e-01 1.30e+01 ... (remaining 12233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.62: 4876 16.62 - 33.23: 384 33.23 - 49.85: 55 49.85 - 66.46: 13 66.46 - 83.08: 8 Dihedral angle restraints: 5336 sinusoidal: 2000 harmonic: 3336 Sorted by residual: dihedral pdb=" CB CYS B 121 " pdb=" SG CYS B 121 " pdb=" SG CYS B 149 " pdb=" CB CYS B 149 " ideal model delta sinusoidal sigma weight residual 93.00 149.62 -56.62 1 1.00e+01 1.00e-02 4.32e+01 dihedral pdb=" CA LEU D 200 " pdb=" C LEU D 200 " pdb=" N PRO D 201 " pdb=" CA PRO D 201 " ideal model delta harmonic sigma weight residual -180.00 -152.44 -27.56 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 153.31 26.69 0 5.00e+00 4.00e-02 2.85e+01 ... (remaining 5333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1296 0.079 - 0.159: 110 0.159 - 0.238: 3 0.238 - 0.317: 0 0.317 - 0.397: 1 Chirality restraints: 1410 Sorted by residual: chirality pdb=" CA THR A 329 " pdb=" N THR A 329 " pdb=" C THR A 329 " pdb=" CB THR A 329 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA GLN D 153 " pdb=" N GLN D 153 " pdb=" C GLN D 153 " pdb=" CB GLN D 153 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA THR A 327 " pdb=" N THR A 327 " pdb=" C THR A 327 " pdb=" CB THR A 327 " both_signs ideal model delta sigma weight residual False 2.53 2.70 -0.17 2.00e-01 2.50e+01 7.47e-01 ... (remaining 1407 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 214 " -0.021 2.00e-02 2.50e+03 4.30e-02 1.85e+01 pdb=" C LEU D 214 " 0.074 2.00e-02 2.50e+03 pdb=" O LEU D 214 " -0.028 2.00e-02 2.50e+03 pdb=" N LEU D 215 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 325 " -0.021 2.00e-02 2.50e+03 4.18e-02 1.75e+01 pdb=" C CYS A 325 " 0.072 2.00e-02 2.50e+03 pdb=" O CYS A 325 " -0.027 2.00e-02 2.50e+03 pdb=" N SER A 326 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 105 " 0.007 2.00e-02 2.50e+03 2.47e-02 1.22e+01 pdb=" CG TYR B 105 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 105 " -0.036 2.00e-02 2.50e+03 pdb=" CD2 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 105 " 0.037 2.00e-02 2.50e+03 pdb=" CE2 TYR B 105 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 105 " 0.032 2.00e-02 2.50e+03 pdb=" OH TYR B 105 " -0.032 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2192 2.80 - 3.33: 8739 3.33 - 3.85: 15043 3.85 - 4.38: 17994 4.38 - 4.90: 30345 Nonbonded interactions: 74313 Sorted by model distance: nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.278 2.440 nonbonded pdb=" OD1 ASN D 304 " pdb=" NZ LYS D 308 " model vdw 2.283 2.520 nonbonded pdb=" O ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.283 2.520 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.348 2.440 nonbonded pdb=" OG SER H 161 " pdb=" O LYS H 163 " model vdw 2.360 2.440 ... (remaining 74308 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.760 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 27.020 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 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 : 0.004 0.173 9022 Z= 0.233 Angle : 0.680 9.633 12238 Z= 0.411 Chirality : 0.045 0.397 1410 Planarity : 0.007 0.057 1537 Dihedral : 12.747 83.080 3172 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 0.74 % Allowed : 2.33 % Favored : 96.93 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1127 helix: -1.09 (0.22), residues: 406 sheet: -0.18 (0.30), residues: 277 loop : -1.01 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.022 0.002 PHE D 354 TYR 0.037 0.005 TYR B 105 ARG 0.053 0.008 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 317 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7824 (ttpt) cc_final: 0.7518 (ttpt) REVERT: A 33 GLU cc_start: 0.6880 (mt-10) cc_final: 0.6426 (mt-10) REVERT: A 186 GLU cc_start: 0.6591 (tt0) cc_final: 0.5926 (tt0) REVERT: A 197 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7524 (mtpp) REVERT: A 210 LYS cc_start: 0.7691 (mmmt) cc_final: 0.7453 (mmtt) REVERT: A 243 MET cc_start: 0.7404 (tpp) cc_final: 0.7156 (tpp) REVERT: A 272 ASP cc_start: 0.7260 (t0) cc_final: 0.6936 (t0) REVERT: A 330 LYS cc_start: 0.6983 (mmtt) cc_final: 0.6424 (mmtt) REVERT: B 43 ILE cc_start: 0.8993 (mm) cc_final: 0.8747 (mt) REVERT: B 83 ASP cc_start: 0.6948 (t0) cc_final: 0.6418 (t0) REVERT: B 121 CYS cc_start: 0.6087 (t) cc_final: 0.5699 (t) REVERT: B 188 MET cc_start: 0.7480 (mmm) cc_final: 0.7132 (mmm) REVERT: B 204 CYS cc_start: 0.7584 (m) cc_final: 0.7309 (m) REVERT: B 205 ASP cc_start: 0.7097 (p0) cc_final: 0.6852 (p0) REVERT: B 219 ARG cc_start: 0.6994 (mmt180) cc_final: 0.6775 (mmt-90) REVERT: B 228 ASP cc_start: 0.5841 (t0) cc_final: 0.5626 (t70) REVERT: B 232 ILE cc_start: 0.8525 (tt) cc_final: 0.8196 (tt) REVERT: B 239 ASN cc_start: 0.7401 (m-40) cc_final: 0.7189 (m-40) REVERT: B 261 LEU cc_start: 0.8006 (mp) cc_final: 0.7803 (mt) REVERT: B 277 SER cc_start: 0.8371 (t) cc_final: 0.7748 (m) REVERT: B 312 ASP cc_start: 0.5952 (t0) cc_final: 0.5590 (t70) REVERT: B 322 ASP cc_start: 0.6255 (t0) cc_final: 0.6038 (t0) REVERT: B 333 ASP cc_start: 0.6065 (m-30) cc_final: 0.5609 (m-30) REVERT: D 47 LEU cc_start: 0.7675 (mt) cc_final: 0.7423 (mt) REVERT: D 178 ILE cc_start: 0.7526 (mt) cc_final: 0.7284 (mt) REVERT: D 218 PHE cc_start: 0.7195 (t80) cc_final: 0.6946 (t80) REVERT: D 314 MET cc_start: 0.7046 (tpp) cc_final: 0.6522 (mpp) REVERT: H 94 TYR cc_start: 0.7747 (m-80) cc_final: 0.7327 (m-80) REVERT: H 140 MET cc_start: 0.8153 (mmm) cc_final: 0.7888 (mmm) REVERT: H 173 TYR cc_start: 0.8330 (m-80) cc_final: 0.8067 (m-80) REVERT: H 178 LEU cc_start: 0.8174 (tp) cc_final: 0.7957 (tt) REVERT: H 226 VAL cc_start: 0.7971 (t) cc_final: 0.7670 (m) REVERT: H 243 THR cc_start: 0.8580 (m) cc_final: 0.8336 (p) outliers start: 7 outliers final: 2 residues processed: 322 average time/residue: 0.2136 time to fit residues: 93.1686 Evaluate side-chains 276 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 274 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 326 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 33 optimal weight: 0.0870 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 100 optimal weight: 9.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9022 Z= 0.203 Angle : 0.564 7.301 12238 Z= 0.297 Chirality : 0.042 0.133 1410 Planarity : 0.004 0.044 1537 Dihedral : 5.435 28.592 1236 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.54 % Allowed : 10.81 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.25), residues: 1127 helix: 1.19 (0.26), residues: 401 sheet: -0.20 (0.29), residues: 289 loop : -0.40 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 169 HIS 0.004 0.001 HIS A 195 PHE 0.015 0.002 PHE D 198 TYR 0.012 0.002 TYR D 370 ARG 0.005 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 271 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 LYS cc_start: 0.7669 (ttpt) cc_final: 0.7095 (ttpt) REVERT: A 210 LYS cc_start: 0.7561 (mmmt) cc_final: 0.7114 (mmtt) REVERT: A 261 ASP cc_start: 0.7160 (t0) cc_final: 0.6934 (t0) REVERT: A 272 ASP cc_start: 0.7227 (t0) cc_final: 0.6885 (t0) REVERT: A 314 LYS cc_start: 0.8355 (mmtp) cc_final: 0.8147 (mmtp) REVERT: A 330 LYS cc_start: 0.7092 (mmtt) cc_final: 0.6553 (mmtt) REVERT: B 127 LYS cc_start: 0.8620 (mttm) cc_final: 0.8374 (mttm) REVERT: B 135 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7964 (m) REVERT: B 137 ARG cc_start: 0.7650 (mmt-90) cc_final: 0.7311 (mmt-90) REVERT: B 155 ASN cc_start: 0.7656 (t0) cc_final: 0.7441 (t0) REVERT: B 205 ASP cc_start: 0.7084 (p0) cc_final: 0.6806 (p0) REVERT: B 219 ARG cc_start: 0.7112 (mmt180) cc_final: 0.6878 (mmt90) REVERT: B 261 LEU cc_start: 0.8215 (mp) cc_final: 0.8002 (mp) REVERT: B 275 SER cc_start: 0.8088 (t) cc_final: 0.7805 (m) REVERT: B 277 SER cc_start: 0.8339 (t) cc_final: 0.7732 (m) REVERT: B 312 ASP cc_start: 0.6089 (t0) cc_final: 0.5718 (t70) REVERT: B 331 SER cc_start: 0.8325 (OUTLIER) cc_final: 0.8095 (p) REVERT: B 333 ASP cc_start: 0.6424 (m-30) cc_final: 0.5934 (m-30) REVERT: D 220 ILE cc_start: 0.7777 (mm) cc_final: 0.7529 (mm) REVERT: D 323 PHE cc_start: 0.7866 (m-10) cc_final: 0.7618 (m-80) REVERT: D 369 ILE cc_start: 0.8319 (tp) cc_final: 0.8115 (tt) REVERT: H 94 TYR cc_start: 0.7997 (m-80) cc_final: 0.7723 (m-80) REVERT: H 178 LEU cc_start: 0.8129 (tp) cc_final: 0.7821 (tt) REVERT: H 188 LEU cc_start: 0.8466 (mt) cc_final: 0.8264 (mp) outliers start: 24 outliers final: 15 residues processed: 279 average time/residue: 0.2024 time to fit residues: 78.2135 Evaluate side-chains 286 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 269 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 0.0670 chunk 68 optimal weight: 0.9990 chunk 27 optimal weight: 0.4980 chunk 100 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 0.7980 chunk 99 optimal weight: 0.9990 overall best weight: 0.6722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 131 ASN D 366 ASN G 18 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9022 Z= 0.180 Angle : 0.529 7.212 12238 Z= 0.276 Chirality : 0.041 0.139 1410 Planarity : 0.004 0.047 1537 Dihedral : 4.978 26.501 1235 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.86 % Allowed : 13.35 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.26), residues: 1127 helix: 1.67 (0.26), residues: 404 sheet: -0.27 (0.29), residues: 291 loop : -0.15 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS B 142 PHE 0.018 0.002 PHE D 97 TYR 0.020 0.001 TYR D 179 ARG 0.004 0.000 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 279 time to evaluate : 0.966 Fit side-chains REVERT: A 29 LYS cc_start: 0.7505 (ttpt) cc_final: 0.7262 (ttpt) REVERT: A 33 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6750 (mt-10) REVERT: A 210 LYS cc_start: 0.7531 (mmmt) cc_final: 0.7324 (mmtt) REVERT: A 261 ASP cc_start: 0.7078 (t0) cc_final: 0.6804 (t0) REVERT: A 272 ASP cc_start: 0.7227 (t0) cc_final: 0.6864 (t0) REVERT: A 324 THR cc_start: 0.7916 (m) cc_final: 0.7711 (m) REVERT: A 330 LYS cc_start: 0.7133 (mmtt) cc_final: 0.6589 (mmtt) REVERT: B 135 VAL cc_start: 0.8368 (OUTLIER) cc_final: 0.8120 (m) REVERT: B 155 ASN cc_start: 0.7679 (t0) cc_final: 0.7444 (t0) REVERT: B 165 THR cc_start: 0.7483 (p) cc_final: 0.7070 (t) REVERT: B 205 ASP cc_start: 0.7038 (p0) cc_final: 0.6762 (p0) REVERT: B 219 ARG cc_start: 0.7079 (mmt180) cc_final: 0.6852 (mmt90) REVERT: B 232 ILE cc_start: 0.8535 (tt) cc_final: 0.8167 (tt) REVERT: B 239 ASN cc_start: 0.7428 (m-40) cc_final: 0.7150 (m-40) REVERT: B 263 THR cc_start: 0.8246 (m) cc_final: 0.8028 (p) REVERT: B 275 SER cc_start: 0.7993 (t) cc_final: 0.7686 (m) REVERT: B 312 ASP cc_start: 0.6151 (t0) cc_final: 0.5811 (t70) REVERT: B 333 ASP cc_start: 0.6307 (m-30) cc_final: 0.5865 (m-30) REVERT: D 154 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8101 (p) REVERT: D 220 ILE cc_start: 0.7815 (mm) cc_final: 0.7567 (mm) REVERT: D 369 ILE cc_start: 0.8348 (tp) cc_final: 0.8141 (tt) REVERT: H 60 TYR cc_start: 0.8058 (m-80) cc_final: 0.7679 (m-80) REVERT: H 173 TYR cc_start: 0.8514 (m-80) cc_final: 0.8304 (m-80) REVERT: H 178 LEU cc_start: 0.8218 (tp) cc_final: 0.7990 (tt) REVERT: H 243 THR cc_start: 0.8612 (m) cc_final: 0.8169 (p) outliers start: 27 outliers final: 20 residues processed: 286 average time/residue: 0.2168 time to fit residues: 84.1557 Evaluate side-chains 275 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 253 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN D 44 GLN D 77 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9022 Z= 0.218 Angle : 0.534 7.088 12238 Z= 0.278 Chirality : 0.042 0.131 1410 Planarity : 0.004 0.044 1537 Dihedral : 4.809 25.798 1235 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.71 % Allowed : 14.83 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.25), residues: 1127 helix: 1.71 (0.26), residues: 411 sheet: -0.32 (0.29), residues: 290 loop : -0.02 (0.32), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 297 HIS 0.004 0.001 HIS B 225 PHE 0.013 0.002 PHE D 198 TYR 0.016 0.002 TYR D 179 ARG 0.009 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 256 time to evaluate : 0.950 Fit side-chains REVERT: A 29 LYS cc_start: 0.7534 (ttpt) cc_final: 0.7128 (ttpt) REVERT: A 33 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6562 (mt-10) REVERT: A 197 LYS cc_start: 0.7993 (mtpp) cc_final: 0.7774 (mtpp) REVERT: A 261 ASP cc_start: 0.7099 (t0) cc_final: 0.6825 (t0) REVERT: A 269 ASN cc_start: 0.7932 (m-40) cc_final: 0.7608 (m-40) REVERT: A 272 ASP cc_start: 0.7204 (t0) cc_final: 0.6842 (t0) REVERT: A 324 THR cc_start: 0.7887 (m) cc_final: 0.7619 (m) REVERT: A 330 LYS cc_start: 0.7157 (mmtt) cc_final: 0.6620 (mmtt) REVERT: B 52 ARG cc_start: 0.6943 (mtp85) cc_final: 0.6715 (mtm-85) REVERT: B 135 VAL cc_start: 0.8461 (OUTLIER) cc_final: 0.8248 (m) REVERT: B 150 ARG cc_start: 0.7847 (mmt-90) cc_final: 0.7493 (mmt-90) REVERT: B 155 ASN cc_start: 0.7694 (t0) cc_final: 0.7475 (t0) REVERT: B 165 THR cc_start: 0.7429 (p) cc_final: 0.7007 (t) REVERT: B 168 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7150 (tp) REVERT: B 219 ARG cc_start: 0.7154 (mmt180) cc_final: 0.6859 (mmt-90) REVERT: B 228 ASP cc_start: 0.5874 (t70) cc_final: 0.5658 (t70) REVERT: B 239 ASN cc_start: 0.7449 (m-40) cc_final: 0.7097 (m-40) REVERT: B 258 ASP cc_start: 0.7202 (t0) cc_final: 0.6761 (t0) REVERT: B 263 THR cc_start: 0.8300 (m) cc_final: 0.8091 (p) REVERT: B 275 SER cc_start: 0.8026 (t) cc_final: 0.7691 (m) REVERT: B 298 ASP cc_start: 0.7116 (t70) cc_final: 0.6795 (t70) REVERT: B 301 LYS cc_start: 0.8250 (mmmt) cc_final: 0.8020 (mtpp) REVERT: B 333 ASP cc_start: 0.6263 (m-30) cc_final: 0.5693 (m-30) REVERT: D 154 THR cc_start: 0.8358 (OUTLIER) cc_final: 0.8150 (p) REVERT: D 220 ILE cc_start: 0.7866 (mm) cc_final: 0.7617 (mm) REVERT: D 369 ILE cc_start: 0.8398 (tp) cc_final: 0.8197 (tt) REVERT: H 60 TYR cc_start: 0.8072 (m-80) cc_final: 0.7740 (m-80) REVERT: H 166 LEU cc_start: 0.8418 (tp) cc_final: 0.8202 (tt) REVERT: H 172 THR cc_start: 0.8292 (m) cc_final: 0.7946 (p) REVERT: H 173 TYR cc_start: 0.8535 (m-80) cc_final: 0.8289 (m-80) REVERT: H 178 LEU cc_start: 0.8258 (tp) cc_final: 0.8005 (tt) REVERT: H 243 THR cc_start: 0.8598 (m) cc_final: 0.8103 (p) outliers start: 35 outliers final: 25 residues processed: 267 average time/residue: 0.2091 time to fit residues: 76.4755 Evaluate side-chains 275 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 247 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 154 THR Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 74 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.0670 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9022 Z= 0.187 Angle : 0.514 6.924 12238 Z= 0.267 Chirality : 0.041 0.133 1410 Planarity : 0.004 0.046 1537 Dihedral : 4.645 24.671 1235 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.13 % Allowed : 16.31 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1127 helix: 2.13 (0.26), residues: 394 sheet: -0.26 (0.29), residues: 286 loop : -0.01 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS B 225 PHE 0.018 0.002 PHE D 198 TYR 0.027 0.001 TYR D 179 ARG 0.006 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 250 time to evaluate : 0.932 Fit side-chains REVERT: A 29 LYS cc_start: 0.7509 (ttpt) cc_final: 0.7013 (ttpt) REVERT: A 33 GLU cc_start: 0.6821 (mt-10) cc_final: 0.6418 (mt-10) REVERT: A 197 LYS cc_start: 0.8061 (mtpp) cc_final: 0.7760 (mtpp) REVERT: A 257 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7788 (mtmm) REVERT: A 261 ASP cc_start: 0.7089 (t0) cc_final: 0.6793 (t0) REVERT: A 269 ASN cc_start: 0.7981 (m-40) cc_final: 0.7588 (m-40) REVERT: A 324 THR cc_start: 0.7828 (m) cc_final: 0.7510 (m) REVERT: A 330 LYS cc_start: 0.7173 (mmtt) cc_final: 0.6648 (mmtt) REVERT: B 52 ARG cc_start: 0.6851 (mtp85) cc_final: 0.6597 (mtm-85) REVERT: B 135 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8248 (m) REVERT: B 165 THR cc_start: 0.7297 (p) cc_final: 0.6857 (t) REVERT: B 219 ARG cc_start: 0.7175 (mmt180) cc_final: 0.6854 (mmt90) REVERT: B 232 ILE cc_start: 0.8510 (tt) cc_final: 0.8149 (tt) REVERT: B 239 ASN cc_start: 0.7391 (m-40) cc_final: 0.7117 (m-40) REVERT: B 255 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7740 (mt) REVERT: B 258 ASP cc_start: 0.7255 (t0) cc_final: 0.6703 (t0) REVERT: B 275 SER cc_start: 0.7980 (t) cc_final: 0.7658 (m) REVERT: B 298 ASP cc_start: 0.7191 (t70) cc_final: 0.6898 (t0) REVERT: B 300 LEU cc_start: 0.8113 (mt) cc_final: 0.7877 (mp) REVERT: B 301 LYS cc_start: 0.8229 (mmmt) cc_final: 0.7978 (mtpp) REVERT: B 333 ASP cc_start: 0.5965 (m-30) cc_final: 0.5648 (m-30) REVERT: D 212 PHE cc_start: 0.7215 (t80) cc_final: 0.6976 (t80) REVERT: H 60 TYR cc_start: 0.8019 (m-80) cc_final: 0.7727 (m-80) REVERT: H 172 THR cc_start: 0.8277 (m) cc_final: 0.8035 (p) REVERT: H 178 LEU cc_start: 0.8276 (tp) cc_final: 0.8025 (tt) REVERT: H 215 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7110 (p) outliers start: 39 outliers final: 26 residues processed: 264 average time/residue: 0.1910 time to fit residues: 70.4656 Evaluate side-chains 267 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 237 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 329 ILE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 107 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN D 77 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9022 Z= 0.187 Angle : 0.517 6.937 12238 Z= 0.267 Chirality : 0.041 0.171 1410 Planarity : 0.004 0.044 1537 Dihedral : 4.563 24.611 1235 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 4.24 % Allowed : 17.06 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.26), residues: 1127 helix: 2.03 (0.26), residues: 404 sheet: -0.19 (0.29), residues: 286 loop : -0.13 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 297 HIS 0.005 0.001 HIS B 225 PHE 0.016 0.002 PHE D 198 TYR 0.020 0.001 TYR D 179 ARG 0.006 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 254 time to evaluate : 1.035 Fit side-chains REVERT: A 23 LEU cc_start: 0.7259 (mt) cc_final: 0.6985 (mp) REVERT: A 29 LYS cc_start: 0.7498 (ttpt) cc_final: 0.6970 (ttpt) REVERT: A 33 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6386 (mt-10) REVERT: A 197 LYS cc_start: 0.8053 (mtpp) cc_final: 0.7734 (mtpp) REVERT: A 251 ASP cc_start: 0.7104 (t0) cc_final: 0.6871 (t0) REVERT: A 257 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7818 (mtmm) REVERT: A 261 ASP cc_start: 0.7181 (t0) cc_final: 0.6870 (t0) REVERT: A 269 ASN cc_start: 0.7980 (m-40) cc_final: 0.7571 (m-40) REVERT: A 309 ASP cc_start: 0.6453 (m-30) cc_final: 0.6072 (m-30) REVERT: A 324 THR cc_start: 0.7805 (m) cc_final: 0.7515 (m) REVERT: A 330 LYS cc_start: 0.7161 (mmtt) cc_final: 0.6670 (mmtt) REVERT: B 135 VAL cc_start: 0.8486 (OUTLIER) cc_final: 0.8267 (m) REVERT: B 150 ARG cc_start: 0.7892 (mmt-90) cc_final: 0.7485 (mmt-90) REVERT: B 219 ARG cc_start: 0.7177 (mmt180) cc_final: 0.6774 (mmt-90) REVERT: B 232 ILE cc_start: 0.8514 (tt) cc_final: 0.8154 (tt) REVERT: B 239 ASN cc_start: 0.7377 (m-40) cc_final: 0.6941 (m-40) REVERT: B 256 ARG cc_start: 0.7902 (mpp80) cc_final: 0.7353 (mtm-85) REVERT: B 275 SER cc_start: 0.7985 (t) cc_final: 0.7663 (m) REVERT: B 298 ASP cc_start: 0.7215 (t70) cc_final: 0.6983 (t0) REVERT: B 300 LEU cc_start: 0.8128 (mt) cc_final: 0.7867 (mp) REVERT: D 212 PHE cc_start: 0.7209 (t80) cc_final: 0.6872 (t80) REVERT: H 172 THR cc_start: 0.8277 (m) cc_final: 0.8011 (p) REVERT: H 178 LEU cc_start: 0.8264 (tp) cc_final: 0.8031 (tt) REVERT: H 215 THR cc_start: 0.7451 (OUTLIER) cc_final: 0.7119 (p) outliers start: 40 outliers final: 28 residues processed: 267 average time/residue: 0.2036 time to fit residues: 75.8084 Evaluate side-chains 273 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 0.0020 chunk 90 optimal weight: 5.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN D 98 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9022 Z= 0.180 Angle : 0.533 7.246 12238 Z= 0.269 Chirality : 0.042 0.215 1410 Planarity : 0.004 0.045 1537 Dihedral : 4.542 25.958 1235 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.60 % Allowed : 19.28 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1127 helix: 2.12 (0.26), residues: 404 sheet: -0.19 (0.29), residues: 282 loop : -0.06 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 111 HIS 0.005 0.001 HIS B 225 PHE 0.020 0.002 PHE H 68 TYR 0.024 0.001 TYR D 179 ARG 0.005 0.000 ARG H 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 242 time to evaluate : 1.042 Fit side-chains REVERT: A 29 LYS cc_start: 0.7469 (ttpt) cc_final: 0.6969 (ttpt) REVERT: A 33 GLU cc_start: 0.6800 (mt-10) cc_final: 0.6370 (mt-10) REVERT: A 197 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7776 (mtpp) REVERT: A 251 ASP cc_start: 0.7137 (t0) cc_final: 0.6882 (t0) REVERT: A 257 LYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7814 (mtmm) REVERT: A 261 ASP cc_start: 0.7178 (t0) cc_final: 0.6853 (t0) REVERT: A 269 ASN cc_start: 0.7952 (m-40) cc_final: 0.7557 (m-40) REVERT: A 309 ASP cc_start: 0.6434 (m-30) cc_final: 0.6087 (m-30) REVERT: A 324 THR cc_start: 0.7784 (m) cc_final: 0.7493 (m) REVERT: A 330 LYS cc_start: 0.7181 (mmtt) cc_final: 0.6676 (mmtt) REVERT: A 333 GLN cc_start: 0.7469 (tp40) cc_final: 0.6982 (tp40) REVERT: B 101 MET cc_start: 0.7971 (ptp) cc_final: 0.7647 (mtp) REVERT: B 135 VAL cc_start: 0.8489 (OUTLIER) cc_final: 0.8271 (m) REVERT: B 210 LEU cc_start: 0.7576 (tp) cc_final: 0.7363 (tp) REVERT: B 219 ARG cc_start: 0.7166 (mmt180) cc_final: 0.6838 (mmt90) REVERT: B 232 ILE cc_start: 0.8499 (tt) cc_final: 0.8137 (tt) REVERT: B 254 ASP cc_start: 0.6591 (t70) cc_final: 0.6300 (t70) REVERT: B 256 ARG cc_start: 0.7815 (mpp80) cc_final: 0.7218 (mtt180) REVERT: B 275 SER cc_start: 0.7971 (t) cc_final: 0.7664 (m) REVERT: B 298 ASP cc_start: 0.7213 (t70) cc_final: 0.6982 (t0) REVERT: B 300 LEU cc_start: 0.8130 (mt) cc_final: 0.7854 (mp) REVERT: D 162 ILE cc_start: 0.7305 (mt) cc_final: 0.7076 (tt) REVERT: D 212 PHE cc_start: 0.7155 (t80) cc_final: 0.6895 (t80) REVERT: H 155 VAL cc_start: 0.8474 (OUTLIER) cc_final: 0.8139 (m) REVERT: H 172 THR cc_start: 0.8272 (m) cc_final: 0.7967 (p) REVERT: H 178 LEU cc_start: 0.8256 (tp) cc_final: 0.8017 (tt) REVERT: H 215 THR cc_start: 0.7449 (OUTLIER) cc_final: 0.7136 (p) outliers start: 34 outliers final: 26 residues processed: 254 average time/residue: 0.1896 time to fit residues: 67.5861 Evaluate side-chains 271 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 241 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 98 ASN Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 72 optimal weight: 0.0980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 93 optimal weight: 0.4980 chunk 99 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9022 Z= 0.194 Angle : 0.532 7.668 12238 Z= 0.270 Chirality : 0.042 0.165 1410 Planarity : 0.004 0.045 1537 Dihedral : 4.542 27.125 1235 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 3.39 % Allowed : 19.60 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1127 helix: 2.06 (0.26), residues: 405 sheet: -0.22 (0.29), residues: 292 loop : 0.02 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.016 0.002 PHE H 68 TYR 0.021 0.001 TYR D 179 ARG 0.003 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 237 time to evaluate : 0.917 Fit side-chains REVERT: A 10 LYS cc_start: 0.7122 (mmtt) cc_final: 0.6394 (ttmm) REVERT: A 29 LYS cc_start: 0.7354 (ttpt) cc_final: 0.6883 (ttpt) REVERT: A 33 GLU cc_start: 0.6796 (mt-10) cc_final: 0.6369 (mt-10) REVERT: A 197 LYS cc_start: 0.8038 (mtpp) cc_final: 0.7771 (mtpp) REVERT: A 251 ASP cc_start: 0.7166 (t0) cc_final: 0.6911 (t0) REVERT: A 261 ASP cc_start: 0.7168 (t0) cc_final: 0.6849 (t0) REVERT: A 269 ASN cc_start: 0.7934 (m-40) cc_final: 0.7562 (m-40) REVERT: A 309 ASP cc_start: 0.6395 (m-30) cc_final: 0.6095 (m-30) REVERT: A 324 THR cc_start: 0.7766 (m) cc_final: 0.7489 (m) REVERT: A 330 LYS cc_start: 0.7177 (mmtt) cc_final: 0.6668 (mmtt) REVERT: A 333 GLN cc_start: 0.7510 (tp40) cc_final: 0.6983 (tp40) REVERT: B 101 MET cc_start: 0.7950 (ptp) cc_final: 0.7672 (mtp) REVERT: B 135 VAL cc_start: 0.8526 (OUTLIER) cc_final: 0.8312 (m) REVERT: B 165 THR cc_start: 0.7156 (p) cc_final: 0.6729 (t) REVERT: B 188 MET cc_start: 0.7474 (mmm) cc_final: 0.7008 (mmm) REVERT: B 219 ARG cc_start: 0.7058 (mmt180) cc_final: 0.6699 (mmt-90) REVERT: B 232 ILE cc_start: 0.8507 (tt) cc_final: 0.8133 (tt) REVERT: B 254 ASP cc_start: 0.6595 (t70) cc_final: 0.6307 (t70) REVERT: B 258 ASP cc_start: 0.7355 (t0) cc_final: 0.6765 (t0) REVERT: B 275 SER cc_start: 0.8002 (t) cc_final: 0.7681 (m) REVERT: B 298 ASP cc_start: 0.7202 (t70) cc_final: 0.6986 (t0) REVERT: D 102 ASN cc_start: 0.8104 (OUTLIER) cc_final: 0.7818 (t0) REVERT: D 162 ILE cc_start: 0.7311 (mt) cc_final: 0.7092 (tt) REVERT: D 212 PHE cc_start: 0.7166 (t80) cc_final: 0.6909 (t80) REVERT: H 172 THR cc_start: 0.8271 (m) cc_final: 0.7943 (p) REVERT: H 178 LEU cc_start: 0.8254 (tp) cc_final: 0.8022 (tt) REVERT: H 215 THR cc_start: 0.7473 (OUTLIER) cc_final: 0.7155 (p) outliers start: 32 outliers final: 27 residues processed: 249 average time/residue: 0.2208 time to fit residues: 76.2504 Evaluate side-chains 265 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 235 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 77 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9022 Z= 0.207 Angle : 0.542 7.131 12238 Z= 0.275 Chirality : 0.043 0.221 1410 Planarity : 0.004 0.045 1537 Dihedral : 4.504 28.890 1231 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.92 % Allowed : 18.96 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1127 helix: 2.07 (0.26), residues: 404 sheet: -0.22 (0.29), residues: 293 loop : 0.01 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 111 HIS 0.003 0.001 HIS B 225 PHE 0.023 0.002 PHE H 68 TYR 0.020 0.001 TYR D 179 ARG 0.004 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 240 time to evaluate : 0.985 Fit side-chains REVERT: A 10 LYS cc_start: 0.7135 (mmtt) cc_final: 0.6444 (ttmm) REVERT: A 29 LYS cc_start: 0.7349 (ttpt) cc_final: 0.6892 (ttpt) REVERT: A 33 GLU cc_start: 0.6786 (mt-10) cc_final: 0.6376 (mt-10) REVERT: A 197 LYS cc_start: 0.8059 (mtpp) cc_final: 0.7717 (mtpp) REVERT: A 251 ASP cc_start: 0.7202 (t0) cc_final: 0.6928 (t0) REVERT: A 261 ASP cc_start: 0.7156 (t0) cc_final: 0.6810 (t0) REVERT: A 269 ASN cc_start: 0.7931 (m-40) cc_final: 0.7565 (m-40) REVERT: A 309 ASP cc_start: 0.6425 (m-30) cc_final: 0.6165 (m-30) REVERT: A 324 THR cc_start: 0.7759 (m) cc_final: 0.7472 (m) REVERT: A 330 LYS cc_start: 0.7200 (mmtt) cc_final: 0.6731 (mmtt) REVERT: A 333 GLN cc_start: 0.7536 (tp40) cc_final: 0.7002 (tp40) REVERT: B 101 MET cc_start: 0.7945 (ptp) cc_final: 0.7720 (mtp) REVERT: B 135 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8327 (m) REVERT: B 150 ARG cc_start: 0.7891 (mmt-90) cc_final: 0.7479 (mmt-90) REVERT: B 165 THR cc_start: 0.7179 (p) cc_final: 0.6757 (t) REVERT: B 188 MET cc_start: 0.7469 (mmm) cc_final: 0.6983 (mmm) REVERT: B 232 ILE cc_start: 0.8517 (tt) cc_final: 0.8150 (tt) REVERT: B 254 ASP cc_start: 0.6606 (t70) cc_final: 0.6309 (t70) REVERT: B 258 ASP cc_start: 0.7355 (t0) cc_final: 0.6738 (t0) REVERT: B 275 SER cc_start: 0.8031 (t) cc_final: 0.7710 (m) REVERT: B 298 ASP cc_start: 0.7178 (t70) cc_final: 0.6902 (t0) REVERT: D 102 ASN cc_start: 0.8122 (OUTLIER) cc_final: 0.7840 (t0) REVERT: D 162 ILE cc_start: 0.7335 (mt) cc_final: 0.7122 (tt) REVERT: D 212 PHE cc_start: 0.7177 (t80) cc_final: 0.6903 (t80) REVERT: H 139 VAL cc_start: 0.7828 (t) cc_final: 0.7623 (p) REVERT: H 172 THR cc_start: 0.8252 (m) cc_final: 0.7647 (p) REVERT: H 178 LEU cc_start: 0.8275 (tp) cc_final: 0.8031 (tt) REVERT: H 192 MET cc_start: 0.7088 (ttp) cc_final: 0.6604 (ttp) REVERT: H 215 THR cc_start: 0.7499 (OUTLIER) cc_final: 0.7184 (p) outliers start: 37 outliers final: 31 residues processed: 254 average time/residue: 0.2028 time to fit residues: 71.1905 Evaluate side-chains 270 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 236 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 226 MET Chi-restraints excluded: chain D residue 356 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 215 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 88 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 0.0770 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9022 Z= 0.200 Angle : 0.561 8.559 12238 Z= 0.282 Chirality : 0.043 0.311 1410 Planarity : 0.004 0.045 1537 Dihedral : 4.467 30.078 1231 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.39 % Allowed : 19.70 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1127 helix: 2.03 (0.26), residues: 405 sheet: -0.17 (0.30), residues: 293 loop : 0.02 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 111 HIS 0.003 0.001 HIS B 225 PHE 0.021 0.002 PHE H 68 TYR 0.021 0.001 TYR D 179 ARG 0.007 0.000 ARG B 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2254 Ramachandran restraints generated. 1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 229 time to evaluate : 0.959 Fit side-chains REVERT: A 10 LYS cc_start: 0.7121 (mmtt) cc_final: 0.6440 (ttmm) REVERT: A 29 LYS cc_start: 0.7320 (ttpt) cc_final: 0.6892 (ttpt) REVERT: A 33 GLU cc_start: 0.6775 (mt-10) cc_final: 0.6377 (mt-10) REVERT: A 197 LYS cc_start: 0.8044 (mtpp) cc_final: 0.7709 (mtpp) REVERT: A 251 ASP cc_start: 0.7218 (t0) cc_final: 0.6965 (t0) REVERT: A 269 ASN cc_start: 0.7900 (m-40) cc_final: 0.7561 (m-40) REVERT: A 309 ASP cc_start: 0.6389 (m-30) cc_final: 0.6188 (m-30) REVERT: A 324 THR cc_start: 0.7749 (m) cc_final: 0.7469 (m) REVERT: A 330 LYS cc_start: 0.7202 (mmtt) cc_final: 0.6740 (mmtt) REVERT: A 333 GLN cc_start: 0.7537 (tp40) cc_final: 0.7335 (tp40) REVERT: B 101 MET cc_start: 0.7935 (ptp) cc_final: 0.7725 (mtp) REVERT: B 135 VAL cc_start: 0.8524 (OUTLIER) cc_final: 0.8312 (m) REVERT: B 150 ARG cc_start: 0.7897 (mmt-90) cc_final: 0.7472 (mmt-90) REVERT: B 165 THR cc_start: 0.7133 (p) cc_final: 0.6768 (t) REVERT: B 188 MET cc_start: 0.7464 (mmm) cc_final: 0.6966 (mmm) REVERT: B 254 ASP cc_start: 0.6632 (t70) cc_final: 0.6335 (t70) REVERT: B 258 ASP cc_start: 0.7344 (t0) cc_final: 0.6697 (t0) REVERT: B 275 SER cc_start: 0.8018 (t) cc_final: 0.7715 (m) REVERT: D 95 MET cc_start: 0.6914 (mtm) cc_final: 0.6692 (mtm) REVERT: D 102 ASN cc_start: 0.8110 (OUTLIER) cc_final: 0.7855 (t0) REVERT: D 162 ILE cc_start: 0.7356 (mt) cc_final: 0.7153 (tt) REVERT: D 212 PHE cc_start: 0.7167 (t80) cc_final: 0.6878 (t80) REVERT: H 172 THR cc_start: 0.8251 (m) cc_final: 0.7867 (p) REVERT: H 178 LEU cc_start: 0.8271 (tp) cc_final: 0.8031 (tt) REVERT: H 215 THR cc_start: 0.7505 (OUTLIER) cc_final: 0.7195 (p) outliers start: 32 outliers final: 28 residues processed: 241 average time/residue: 0.2095 time to fit residues: 70.5962 Evaluate side-chains 259 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 228 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 248 LYS Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 102 ASN Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 114 CYS Chi-restraints excluded: chain D residue 159 LEU Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain H residue 57 THR Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 147 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 215 THR Chi-restraints excluded: chain H residue 219 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN ** D 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.143907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.126813 restraints weight = 12363.663| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.03 r_work: 0.3477 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9022 Z= 0.196 Angle : 0.554 8.236 12238 Z= 0.279 Chirality : 0.043 0.300 1410 Planarity : 0.004 0.044 1537 Dihedral : 4.475 31.066 1231 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.50 % Allowed : 19.49 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.26), residues: 1127 helix: 2.03 (0.26), residues: 405 sheet: -0.02 (0.31), residues: 285 loop : -0.00 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 111 HIS 0.003 0.001 HIS B 225 PHE 0.025 0.002 PHE H 68 TYR 0.021 0.001 TYR D 179 ARG 0.009 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2382.86 seconds wall clock time: 43 minutes 56.33 seconds (2636.33 seconds total)