Starting phenix.real_space_refine on Wed Feb 14 08:42:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vih_32009/02_2024/7vih_32009_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vih_32009/02_2024/7vih_32009.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vih_32009/02_2024/7vih_32009.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vih_32009/02_2024/7vih_32009.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vih_32009/02_2024/7vih_32009_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vih_32009/02_2024/7vih_32009_updated.pdb" } resolution = 2.98 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= -0.002 sd= 0.042 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 65 5.16 5 C 5702 2.51 5 N 1510 2.21 5 O 1660 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 137": "OE1" <-> "OE2" Residue "C GLU 58": "OE1" <-> "OE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 62": "OE1" <-> "OE2" Residue "D GLU 8": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 239": "OE1" <-> "OE2" Residue "D GLU 297": "OE1" <-> "OE2" Residue "D GLU 318": "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: 8938 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "E" Number of atoms: 1808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1808 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 10, 'TRANS': 225} Chain breaks: 1 Chain: "F" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2237 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 6, 'TRANS': 272} Chain breaks: 2 Chain: "D" Number of atoms: 1826 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 226, 1820 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 226, 1820 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 2, 'TRANS': 223} Chain breaks: 1 bond proxies already assigned to first conformer: 1843 Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'7I4': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS D 305 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS D 305 " occ=0.50 Time building chain proxies: 7.13, per 1000 atoms: 0.80 Number of scatterers: 8938 At special positions: 0 Unit cell: (105.41, 117.03, 131.14, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 F 1 9.00 O 1660 8.00 N 1510 7.00 C 5702 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Simple disulfide: pdb=" SG CYS F 184 " - pdb=" SG CYS F 191 " distance=2.03 Simple disulfide: pdb=" SG CYS F 282 " - pdb=" SG CYS F 287 " 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: 3.78 Conformation dependent library (CDL) restraints added in 2.4 seconds 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2126 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 34.6% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.34 Creating SS restraints... Processing helix chain 'A' and resid 3 through 23 Processing helix chain 'A' and resid 29 through 34 removed outlier: 3.943A pdb=" N ASN A 34 " --> pdb=" O SER A 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 30 through 43 removed outlier: 3.604A pdb=" N LEU C 37 " --> pdb=" O ALA C 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'E' and resid 221 through 223 No H-bonds generated for 'chain 'E' and resid 221 through 223' Processing helix chain 'F' and resid 24 through 32 Processing helix chain 'F' and resid 49 through 72 Processing helix chain 'F' and resid 79 through 104 Processing helix chain 'F' and resid 106 through 108 No H-bonds generated for 'chain 'F' and resid 106 through 108' Processing helix chain 'F' and resid 114 through 147 Processing helix chain 'F' and resid 157 through 180 removed outlier: 4.068A pdb=" N LEU F 172 " --> pdb=" O TRP F 168 " (cutoff:3.500A) Proline residue: F 178 - end of helix Processing helix chain 'F' and resid 200 through 233 Processing helix chain 'F' and resid 250 through 281 Proline residue: F 271 - end of helix removed outlier: 4.012A pdb=" N VAL F 280 " --> pdb=" O LEU F 276 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLY F 281 " --> pdb=" O LEU F 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 294 through 313 Proline residue: F 308 - end of helix Processing helix chain 'F' and resid 316 through 323 Processing helix chain 'D' and resid 7 through 31 Processing helix chain 'D' and resid 46 through 55 Processing helix chain 'D' and resid 208 through 210 No H-bonds generated for 'chain 'D' and resid 208 through 210' Processing helix chain 'D' and resid 212 through 215 Processing helix chain 'D' and resid 227 through 231 removed outlier: 4.105A pdb=" N ASP D 231 " --> pdb=" O SER D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 254 Processing helix chain 'D' and resid 271 through 280 removed outlier: 3.578A pdb=" N GLU D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS D 279 " --> pdb=" O GLU D 275 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LYS D 280 " --> pdb=" O GLU D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 285 No H-bonds generated for 'chain 'D' and resid 283 through 285' Processing helix chain 'D' and resid 296 through 309 Processing helix chain 'D' and resid 331 through 351 Processing sheet with id= A, first strand: chain 'A' and resid 57 through 61 removed outlier: 6.957A pdb=" N ALA A 72 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N MET A 60 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 70 " --> pdb=" O MET A 60 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER A 73 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS A 77 " --> pdb=" O SER A 73 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS A 90 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ASP A 82 " --> pdb=" O LYS A 88 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N LYS A 88 " --> pdb=" O ASP A 82 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 99 through 104 removed outlier: 6.941A pdb=" N GLY A 114 " --> pdb=" O MET A 100 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N CYS A 102 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ALA A 112 " --> pdb=" O CYS A 102 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TYR A 104 " --> pdb=" O TYR A 110 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N TYR A 110 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLY A 115 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE A 119 " --> pdb=" O GLY A 115 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N ASN A 124 " --> pdb=" O VAL A 134 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL A 134 " --> pdb=" O ASN A 124 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 145 through 150 removed outlier: 6.814A pdb=" N SER A 159 " --> pdb=" O SER A 146 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N CYS A 148 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N VAL A 157 " --> pdb=" O CYS A 148 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N PHE A 150 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N GLN A 155 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP A 169 " --> pdb=" O GLN A 175 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN A 175 " --> pdb=" O ASP A 169 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 186 through 191 removed outlier: 7.046A pdb=" N GLY A 201 " --> pdb=" O MET A 187 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU A 189 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL A 199 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N LEU A 191 " --> pdb=" O LEU A 197 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LEU A 197 " --> pdb=" O LEU A 191 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN A 219 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N ASP A 211 " --> pdb=" O CYS A 217 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N CYS A 217 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 228 through 233 removed outlier: 6.724A pdb=" N GLY A 243 " --> pdb=" O ASN A 229 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE A 231 " --> pdb=" O ALA A 241 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA A 241 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE A 233 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ALA A 239 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASP A 253 " --> pdb=" O GLU A 259 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLU A 259 " --> pdb=" O ASP A 253 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 272 through 277 removed outlier: 6.612A pdb=" N GLY A 287 " --> pdb=" O THR A 273 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL A 275 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU A 285 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N PHE A 277 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LEU A 283 " --> pdb=" O PHE A 277 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASP A 297 " --> pdb=" O ARG A 303 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ARG A 303 " --> pdb=" O ASP A 297 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 45 through 50 removed outlier: 6.759A pdb=" N ILE A 337 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N THR A 49 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU A 335 " --> pdb=" O THR A 49 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'E' and resid 11 through 13 removed outlier: 6.387A pdb=" N THR E 118 " --> pdb=" O VAL E 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'E' and resid 115 through 117 removed outlier: 5.859A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 149 removed outlier: 7.096A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL E 149 " --> pdb=" O LYS E 244 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLU E 246 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 removed outlier: 3.696A pdb=" N THR E 213 " --> pdb=" O SER E 206 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 319 through 322 removed outlier: 6.888A pdb=" N ILE D 264 " --> pdb=" O TYR D 320 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N HIS D 322 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU D 266 " --> pdb=" O HIS D 322 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N HIS D 195 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU D 36 " --> pdb=" O HIS D 195 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS D 197 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU D 38 " --> pdb=" O LYS D 197 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE D 199 " --> pdb=" O LEU D 38 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N GLY D 40 " --> pdb=" O PHE D 199 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1177 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: 3.25 Time building geometry restraints manager: 4.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 1440 1.29 - 1.42: 2402 1.42 - 1.55: 5179 1.55 - 1.68: 5 1.68 - 1.81: 92 Bond restraints: 9118 Sorted by residual: bond pdb=" C16 7I4 F 401 " pdb=" N17 7I4 F 401 " ideal model delta sigma weight residual 1.441 1.154 0.287 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C19 7I4 F 401 " pdb=" C23 7I4 F 401 " ideal model delta sigma weight residual 1.537 1.415 0.122 2.00e-02 2.50e+03 3.69e+01 bond pdb=" C18 7I4 F 401 " pdb=" C19 7I4 F 401 " ideal model delta sigma weight residual 1.533 1.412 0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" N MET D 240 " pdb=" CA MET D 240 " ideal model delta sigma weight residual 1.457 1.528 -0.072 1.24e-02 6.50e+03 3.34e+01 bond pdb=" C19 7I4 F 401 " pdb=" C20 7I4 F 401 " ideal model delta sigma weight residual 1.538 1.637 -0.099 2.00e-02 2.50e+03 2.44e+01 ... (remaining 9113 not shown) Histogram of bond angle deviations from ideal: 89.00 - 99.44: 5 99.44 - 109.88: 1151 109.88 - 120.33: 7287 120.33 - 130.77: 3853 130.77 - 141.21: 44 Bond angle restraints: 12340 Sorted by residual: angle pdb=" N VAL D 233 " pdb=" CA VAL D 233 " pdb=" C VAL D 233 " ideal model delta sigma weight residual 110.53 120.89 -10.36 9.40e-01 1.13e+00 1.21e+02 angle pdb=" N THR F 236 " pdb=" CA THR F 236 " pdb=" C THR F 236 " ideal model delta sigma weight residual 109.76 124.56 -14.80 1.59e+00 3.96e-01 8.67e+01 angle pdb=" C THR F 236 " pdb=" CA THR F 236 " pdb=" CB THR F 236 " ideal model delta sigma weight residual 109.84 98.27 11.57 1.63e+00 3.76e-01 5.04e+01 angle pdb=" N GLU D 236 " pdb=" CA GLU D 236 " pdb=" C GLU D 236 " ideal model delta sigma weight residual 111.14 103.92 7.22 1.08e+00 8.57e-01 4.47e+01 angle pdb=" C TYR F 98 " pdb=" CA TYR F 98 " pdb=" CB TYR F 98 " ideal model delta sigma weight residual 110.79 99.77 11.02 1.66e+00 3.63e-01 4.40e+01 ... (remaining 12335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 5333 35.68 - 71.37: 80 71.37 - 107.05: 9 107.05 - 142.74: 0 142.74 - 178.42: 3 Dihedral angle restraints: 5425 sinusoidal: 2128 harmonic: 3297 Sorted by residual: dihedral pdb=" C TYR F 98 " pdb=" N TYR F 98 " pdb=" CA TYR F 98 " pdb=" CB TYR F 98 " ideal model delta harmonic sigma weight residual -122.60 -109.85 -12.75 0 2.50e+00 1.60e-01 2.60e+01 dihedral pdb=" CB CYS F 184 " pdb=" SG CYS F 184 " pdb=" SG CYS F 191 " pdb=" CB CYS F 191 " ideal model delta sinusoidal sigma weight residual -86.00 -127.90 41.90 1 1.00e+01 1.00e-02 2.45e+01 dihedral pdb=" CB CYS E 22 " pdb=" SG CYS E 22 " pdb=" SG CYS E 96 " pdb=" CB CYS E 96 " ideal model delta sinusoidal sigma weight residual 93.00 52.88 40.12 1 1.00e+01 1.00e-02 2.26e+01 ... (remaining 5422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.151: 1411 1.151 - 2.301: 0 2.301 - 3.452: 0 3.452 - 4.603: 0 4.603 - 5.753: 1 Chirality restraints: 1412 Sorted by residual: chirality pdb=" C19 7I4 F 401 " pdb=" C18 7I4 F 401 " pdb=" C20 7I4 F 401 " pdb=" C23 7I4 F 401 " both_signs ideal model delta sigma weight residual False -2.88 2.88 -5.75 2.00e-01 2.50e+01 8.28e+02 chirality pdb=" CA LEU F 174 " pdb=" N LEU F 174 " pdb=" C LEU F 174 " pdb=" CB LEU F 174 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA VAL F 96 " pdb=" N VAL F 96 " pdb=" C VAL F 96 " pdb=" CB VAL F 96 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 1409 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 307 " 0.092 5.00e-02 4.00e+02 1.35e-01 2.90e+01 pdb=" N PRO F 308 " -0.233 5.00e-02 4.00e+02 pdb=" CA PRO F 308 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO F 308 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 241 " -0.017 2.00e-02 2.50e+03 3.39e-02 1.15e+01 pdb=" C ASN D 241 " 0.059 2.00e-02 2.50e+03 pdb=" O ASN D 241 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG D 242 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 117 " 0.018 2.00e-02 2.50e+03 1.87e-02 8.75e+00 pdb=" CG TRP F 117 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP F 117 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 117 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP F 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 117 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 117 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 117 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP F 117 " 0.001 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 886 2.74 - 3.28: 8909 3.28 - 3.82: 14941 3.82 - 4.36: 18153 4.36 - 4.90: 32074 Nonbonded interactions: 74963 Sorted by model distance: nonbonded pdb=" O GLN A 74 " pdb=" OG SER A 97 " model vdw 2.205 2.440 nonbonded pdb=" OG SER A 244 " pdb=" OD1 ASP A 246 " model vdw 2.228 2.440 nonbonded pdb=" O LYS F 283 " pdb=" OG1 THR F 286 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR E 175 " pdb=" OE2 GLU D 8 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR D 290 " pdb=" O SER D 293 " model vdw 2.237 2.440 ... (remaining 74958 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=0.50 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: 1.090 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: 5.470 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 37.100 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 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: 0.020 Load rotamer database and sin/cos tables:25.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.006 0.287 9118 Z= 0.396 Angle : 0.800 17.898 12340 Z= 0.449 Chirality : 0.161 5.753 1412 Planarity : 0.006 0.135 1544 Dihedral : 13.996 178.421 3287 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.14 % Rotamer: Outliers : 0.61 % Allowed : 0.41 % Favored : 98.98 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % 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: 0.70 (0.24), residues: 1121 helix: 2.00 (0.25), residues: 389 sheet: 0.08 (0.30), residues: 271 loop : -0.58 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP F 117 HIS 0.003 0.001 HIS E 167 PHE 0.021 0.001 PHE A 291 TYR 0.039 0.002 TYR F 98 ARG 0.009 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.007 Fit side-chains REVERT: A 28 THR cc_start: 0.8719 (p) cc_final: 0.8423 (t) REVERT: E 34 MET cc_start: 0.8715 (mmm) cc_final: 0.8396 (mmm) REVERT: F 172 LEU cc_start: 0.6014 (mm) cc_final: 0.5746 (mm) REVERT: F 269 TRP cc_start: 0.7451 (OUTLIER) cc_final: 0.7239 (m100) outliers start: 6 outliers final: 2 residues processed: 164 average time/residue: 1.3413 time to fit residues: 233.0961 Evaluate side-chains 120 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 117 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain D residue 233 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.7980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 HIS A 174 GLN A 292 ASN E 171 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9118 Z= 0.232 Angle : 0.575 8.852 12340 Z= 0.291 Chirality : 0.042 0.219 1412 Planarity : 0.004 0.080 1544 Dihedral : 7.923 150.359 1252 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.37 % Allowed : 10.53 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.24), residues: 1121 helix: 2.16 (0.25), residues: 387 sheet: 0.09 (0.30), residues: 275 loop : -0.46 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS E 167 PHE 0.012 0.001 PHE D 189 TYR 0.035 0.002 TYR E 235 ARG 0.007 0.000 ARG F 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 124 time to evaluate : 1.006 Fit side-chains REVERT: A 28 THR cc_start: 0.8767 (p) cc_final: 0.8424 (t) REVERT: C 47 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.7797 (mt-10) REVERT: E 76 LYS cc_start: 0.8663 (ttmp) cc_final: 0.8389 (mptt) REVERT: E 180 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7872 (mtt90) REVERT: E 186 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.8085 (tt0) REVERT: F 90 SER cc_start: 0.7942 (p) cc_final: 0.7739 (p) REVERT: F 124 MET cc_start: 0.6697 (OUTLIER) cc_final: 0.6495 (mtp) REVERT: F 172 LEU cc_start: 0.6131 (mm) cc_final: 0.5738 (mm) REVERT: F 269 TRP cc_start: 0.7486 (OUTLIER) cc_final: 0.7259 (m100) REVERT: D 240 MET cc_start: 0.5940 (ppp) cc_final: 0.5598 (ppp) REVERT: D 280 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7520 (pttp) outliers start: 33 outliers final: 9 residues processed: 136 average time/residue: 1.1693 time to fit residues: 170.2567 Evaluate side-chains 126 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 112 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 233 VAL Chi-restraints excluded: chain D residue 280 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 83 optimal weight: 0.0870 chunk 68 optimal weight: 0.0050 chunk 27 optimal weight: 0.0870 chunk 100 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 80 optimal weight: 1.9990 overall best weight: 0.6354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 174 GLN A 292 ASN E 39 GLN E 171 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 153 ASN F 156 ASN D 188 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9118 Z= 0.156 Angle : 0.492 6.077 12340 Z= 0.254 Chirality : 0.040 0.193 1412 Planarity : 0.004 0.062 1544 Dihedral : 7.410 137.616 1250 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.97 % Allowed : 13.29 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.05 (0.25), residues: 1121 helix: 2.38 (0.25), residues: 388 sheet: 0.20 (0.30), residues: 269 loop : -0.41 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 117 HIS 0.003 0.000 HIS E 167 PHE 0.011 0.001 PHE A 252 TYR 0.028 0.001 TYR E 235 ARG 0.005 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 28 THR cc_start: 0.8657 (p) cc_final: 0.8405 (t) REVERT: C 47 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7753 (mt-10) REVERT: E 43 LYS cc_start: 0.8080 (ptpt) cc_final: 0.7092 (ptmm) REVERT: E 76 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8400 (mptt) REVERT: E 180 ARG cc_start: 0.8191 (mtt180) cc_final: 0.7975 (mtt90) REVERT: E 220 GLU cc_start: 0.7463 (tt0) cc_final: 0.6751 (tt0) REVERT: F 110 TYR cc_start: 0.4332 (m-10) cc_final: 0.3967 (m-80) REVERT: F 124 MET cc_start: 0.6789 (OUTLIER) cc_final: 0.6572 (mtp) REVERT: F 177 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6653 (tt) REVERT: F 269 TRP cc_start: 0.7448 (OUTLIER) cc_final: 0.7197 (m100) REVERT: D 240 MET cc_start: 0.5943 (ppp) cc_final: 0.5707 (ppp) REVERT: D 280 LYS cc_start: 0.7846 (OUTLIER) cc_final: 0.7509 (pttp) outliers start: 29 outliers final: 12 residues processed: 135 average time/residue: 1.1611 time to fit residues: 167.9325 Evaluate side-chains 134 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 280 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.0040 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN E 39 GLN E 77 ASN E 171 ASN ** F 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9118 Z= 0.181 Angle : 0.483 6.134 12340 Z= 0.254 Chirality : 0.041 0.206 1412 Planarity : 0.004 0.053 1544 Dihedral : 6.524 118.873 1249 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.99 % Allowed : 14.21 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.25), residues: 1121 helix: 2.32 (0.25), residues: 393 sheet: 0.20 (0.30), residues: 270 loop : -0.46 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 168 HIS 0.003 0.001 HIS E 167 PHE 0.011 0.001 PHE D 189 TYR 0.036 0.001 TYR E 235 ARG 0.005 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 121 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 28 THR cc_start: 0.8685 (p) cc_final: 0.8364 (t) REVERT: A 185 ASP cc_start: 0.8655 (OUTLIER) cc_final: 0.8258 (m-30) REVERT: C 47 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7773 (mt-10) REVERT: E 43 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7090 (ptmm) REVERT: E 76 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8387 (mptt) REVERT: E 180 ARG cc_start: 0.8249 (mtt180) cc_final: 0.8016 (mtt90) REVERT: E 186 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: E 220 GLU cc_start: 0.7593 (tt0) cc_final: 0.6709 (tt0) REVERT: F 110 TYR cc_start: 0.4303 (m-10) cc_final: 0.3938 (m-80) REVERT: F 177 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6718 (tt) REVERT: F 269 TRP cc_start: 0.7482 (OUTLIER) cc_final: 0.7180 (m100) REVERT: D 280 LYS cc_start: 0.7856 (OUTLIER) cc_final: 0.7558 (pttp) outliers start: 39 outliers final: 18 residues processed: 138 average time/residue: 1.0667 time to fit residues: 158.7037 Evaluate side-chains 138 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 113 THR Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Chi-restraints excluded: chain D residue 280 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN C 24 ASN E 39 GLN ** E 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 ASN F 101 ASN F 116 GLN F 156 ASN D 188 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 9118 Z= 0.543 Angle : 0.678 7.855 12340 Z= 0.357 Chirality : 0.049 0.286 1412 Planarity : 0.005 0.065 1544 Dihedral : 7.446 123.523 1249 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.81 % Allowed : 14.83 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.42 (0.25), residues: 1121 helix: 1.49 (0.25), residues: 393 sheet: 0.08 (0.31), residues: 272 loop : -0.59 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP F 117 HIS 0.006 0.001 HIS F 28 PHE 0.013 0.002 PHE D 334 TYR 0.047 0.002 TYR E 235 ARG 0.004 0.001 ARG E 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 111 time to evaluate : 1.112 Fit side-chains REVERT: A 233 PHE cc_start: 0.9427 (OUTLIER) cc_final: 0.9037 (m-80) REVERT: C 47 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7919 (mt-10) REVERT: E 43 LYS cc_start: 0.8152 (ptpt) cc_final: 0.7136 (ptmm) REVERT: E 76 LYS cc_start: 0.8745 (OUTLIER) cc_final: 0.8365 (mptt) REVERT: F 110 TYR cc_start: 0.4614 (m-10) cc_final: 0.4056 (m-80) REVERT: F 168 TRP cc_start: 0.8336 (m100) cc_final: 0.8123 (m100) REVERT: F 269 TRP cc_start: 0.7590 (OUTLIER) cc_final: 0.7299 (m100) REVERT: D 209 LYS cc_start: 0.8828 (ptpp) cc_final: 0.8535 (ptmt) outliers start: 47 outliers final: 25 residues processed: 142 average time/residue: 1.1981 time to fit residues: 182.0784 Evaluate side-chains 135 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 47 GLU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 3 GLN Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 186 GLN Chi-restraints excluded: chain E residue 201 ASP Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 247 LEU Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 191 CYS Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 312 THR Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 62 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 102 optimal weight: 0.8980 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 258 GLN E 39 GLN F 156 ASN D 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 9118 Z= 0.190 Angle : 0.509 7.205 12340 Z= 0.269 Chirality : 0.041 0.215 1412 Planarity : 0.004 0.053 1544 Dihedral : 6.245 106.179 1249 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.37 % Allowed : 17.28 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.25), residues: 1121 helix: 1.94 (0.26), residues: 393 sheet: 0.18 (0.31), residues: 270 loop : -0.52 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 117 HIS 0.003 0.000 HIS E 167 PHE 0.011 0.001 PHE A 252 TYR 0.035 0.001 TYR E 235 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 121 time to evaluate : 1.105 Fit side-chains revert: symmetry clash REVERT: A 233 PHE cc_start: 0.9407 (OUTLIER) cc_final: 0.9055 (m-80) REVERT: E 43 LYS cc_start: 0.8055 (ptpt) cc_final: 0.7178 (ptmm) REVERT: E 76 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8317 (mptt) REVERT: F 110 TYR cc_start: 0.4539 (m-10) cc_final: 0.4106 (m-80) REVERT: F 168 TRP cc_start: 0.8266 (m100) cc_final: 0.8049 (m100) REVERT: F 177 LEU cc_start: 0.7173 (OUTLIER) cc_final: 0.6857 (tt) REVERT: F 235 LEU cc_start: 0.6699 (OUTLIER) cc_final: 0.5665 (mt) REVERT: F 292 ARG cc_start: 0.6904 (mpt180) cc_final: 0.5743 (mmm160) REVERT: D 209 LYS cc_start: 0.8783 (ptpp) cc_final: 0.8331 (pttm) outliers start: 33 outliers final: 18 residues processed: 139 average time/residue: 1.1798 time to fit residues: 175.7335 Evaluate side-chains 139 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 117 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 32 THR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.3980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN E 39 GLN E 171 ASN F 101 ASN F 116 GLN D 188 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9118 Z= 0.154 Angle : 0.493 7.567 12340 Z= 0.256 Chirality : 0.040 0.191 1412 Planarity : 0.004 0.057 1544 Dihedral : 5.539 89.899 1249 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 3.37 % Allowed : 18.20 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.94 (0.25), residues: 1121 helix: 2.17 (0.26), residues: 393 sheet: 0.29 (0.31), residues: 269 loop : -0.50 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP F 117 HIS 0.003 0.001 HIS E 167 PHE 0.011 0.001 PHE A 252 TYR 0.031 0.001 TYR E 235 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 126 time to evaluate : 1.069 Fit side-chains REVERT: A 185 ASP cc_start: 0.8651 (OUTLIER) cc_final: 0.8227 (m-30) REVERT: A 233 PHE cc_start: 0.9385 (OUTLIER) cc_final: 0.9030 (m-80) REVERT: E 43 LYS cc_start: 0.8113 (ptpt) cc_final: 0.7109 (ptmm) REVERT: E 76 LYS cc_start: 0.8654 (OUTLIER) cc_final: 0.8337 (mptt) REVERT: F 110 TYR cc_start: 0.4521 (m-10) cc_final: 0.4094 (m-80) REVERT: F 177 LEU cc_start: 0.7090 (OUTLIER) cc_final: 0.6796 (tt) REVERT: F 235 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.5517 (mt) REVERT: D 209 LYS cc_start: 0.8760 (ptpp) cc_final: 0.8315 (pttm) outliers start: 33 outliers final: 19 residues processed: 148 average time/residue: 1.0831 time to fit residues: 172.6236 Evaluate side-chains 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 177 LEU Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.7980 chunk 31 optimal weight: 0.0060 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN E 39 GLN E 171 ASN D 188 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9118 Z= 0.151 Angle : 0.491 8.088 12340 Z= 0.254 Chirality : 0.040 0.188 1412 Planarity : 0.004 0.055 1544 Dihedral : 5.353 81.743 1249 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.58 % Allowed : 18.92 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.25), residues: 1121 helix: 2.28 (0.25), residues: 391 sheet: 0.30 (0.30), residues: 271 loop : -0.48 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP F 117 HIS 0.002 0.000 HIS E 167 PHE 0.011 0.001 PHE A 252 TYR 0.033 0.001 TYR E 235 ARG 0.007 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 125 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 185 ASP cc_start: 0.8627 (OUTLIER) cc_final: 0.8200 (m-30) REVERT: A 233 PHE cc_start: 0.9381 (OUTLIER) cc_final: 0.9032 (m-80) REVERT: E 43 LYS cc_start: 0.8102 (ptpt) cc_final: 0.7100 (ptmm) REVERT: E 76 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8322 (mptt) REVERT: F 110 TYR cc_start: 0.4434 (m-10) cc_final: 0.4061 (m-80) REVERT: F 235 LEU cc_start: 0.6558 (OUTLIER) cc_final: 0.5535 (mt) REVERT: D 209 LYS cc_start: 0.8760 (ptpp) cc_final: 0.8314 (pttm) REVERT: D 333 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7906 (tp-100) outliers start: 35 outliers final: 22 residues processed: 143 average time/residue: 1.1119 time to fit residues: 172.5800 Evaluate side-chains 149 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 123 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 185 ASP Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 192 MET Chi-restraints excluded: chain E residue 194 ASN Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 104 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN E 39 GLN E 171 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9118 Z= 0.319 Angle : 0.583 9.425 12340 Z= 0.303 Chirality : 0.043 0.234 1412 Planarity : 0.005 0.057 1544 Dihedral : 5.914 88.924 1249 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.27 % Allowed : 19.33 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1121 helix: 1.92 (0.25), residues: 391 sheet: 0.17 (0.31), residues: 265 loop : -0.54 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP F 117 HIS 0.004 0.001 HIS F 28 PHE 0.013 0.001 PHE A 252 TYR 0.040 0.002 TYR E 235 ARG 0.005 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 233 PHE cc_start: 0.9411 (OUTLIER) cc_final: 0.8983 (m-80) REVERT: E 43 LYS cc_start: 0.8120 (ptpt) cc_final: 0.7173 (ptmm) REVERT: E 76 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8328 (mptt) REVERT: F 110 TYR cc_start: 0.4567 (m-10) cc_final: 0.4092 (m-80) REVERT: F 124 MET cc_start: 0.6855 (OUTLIER) cc_final: 0.6630 (mtt) REVERT: F 172 LEU cc_start: 0.6110 (mm) cc_final: 0.5670 (mm) REVERT: F 235 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.5594 (mt) REVERT: F 269 TRP cc_start: 0.7532 (OUTLIER) cc_final: 0.7213 (m100) REVERT: D 209 LYS cc_start: 0.8797 (ptpp) cc_final: 0.8349 (pttm) outliers start: 32 outliers final: 22 residues processed: 135 average time/residue: 1.2739 time to fit residues: 184.6303 Evaluate side-chains 143 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 116 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 258 GLN Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 64 ILE Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 87 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN E 39 GLN E 171 ASN F 116 GLN D 188 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9118 Z= 0.195 Angle : 0.543 9.727 12340 Z= 0.281 Chirality : 0.042 0.214 1412 Planarity : 0.004 0.054 1544 Dihedral : 5.684 84.009 1249 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.97 % Allowed : 19.53 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.76 (0.25), residues: 1121 helix: 1.96 (0.25), residues: 391 sheet: 0.25 (0.31), residues: 264 loop : -0.57 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP F 117 HIS 0.003 0.001 HIS E 167 PHE 0.011 0.001 PHE A 252 TYR 0.036 0.001 TYR E 235 ARG 0.011 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2242 Ramachandran restraints generated. 1121 Oldfield, 0 Emsley, 1121 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 123 time to evaluate : 1.010 Fit side-chains revert: symmetry clash REVERT: A 233 PHE cc_start: 0.9404 (OUTLIER) cc_final: 0.9059 (m-80) REVERT: E 43 LYS cc_start: 0.8050 (ptpt) cc_final: 0.7164 (ptmm) REVERT: E 76 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8318 (mptt) REVERT: F 110 TYR cc_start: 0.4572 (m-10) cc_final: 0.4100 (m-80) REVERT: F 124 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6479 (mtt) REVERT: F 172 LEU cc_start: 0.6028 (mm) cc_final: 0.5592 (mm) REVERT: F 235 LEU cc_start: 0.6657 (OUTLIER) cc_final: 0.5562 (mt) REVERT: D 209 LYS cc_start: 0.8780 (ptpp) cc_final: 0.8336 (pttm) outliers start: 29 outliers final: 21 residues processed: 141 average time/residue: 1.1409 time to fit residues: 172.4197 Evaluate side-chains 145 residues out of total 976 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 ASP Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 73 SER Chi-restraints excluded: chain A residue 227 ASP Chi-restraints excluded: chain A residue 233 PHE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain E residue 2 VAL Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 124 MET Chi-restraints excluded: chain F residue 194 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 TRP Chi-restraints excluded: chain F residue 323 ILE Chi-restraints excluded: chain D residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 258 GLN E 39 GLN E 171 ASN ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.144145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.113399 restraints weight = 22567.334| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.93 r_work: 0.3131 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3132 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3132 r_free = 0.3132 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3132 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9118 Z= 0.215 Angle : 0.541 9.625 12340 Z= 0.279 Chirality : 0.042 0.209 1412 Planarity : 0.004 0.057 1544 Dihedral : 5.621 81.996 1249 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.07 % Allowed : 19.53 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.25), residues: 1121 helix: 1.96 (0.25), residues: 390 sheet: 0.19 (0.31), residues: 268 loop : -0.56 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 117 HIS 0.003 0.001 HIS E 167 PHE 0.012 0.001 PHE A 252 TYR 0.036 0.001 TYR E 235 ARG 0.011 0.000 ARG E 160 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3666.09 seconds wall clock time: 66 minutes 16.89 seconds (3976.89 seconds total)