Starting phenix.real_space_refine on Tue Jul 23 20:41:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/07_2024/8unh_42402_neut_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/07_2024/8unh_42402.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/07_2024/8unh_42402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/07_2024/8unh_42402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/07_2024/8unh_42402_neut_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8unh_42402/07_2024/8unh_42402_neut_trim.cif" } resolution = 3.21 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 12960 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 67 5.16 5 C 8409 2.51 5 N 2218 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "E GLU 167": "OE1" <-> "OE2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E TYR 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13244 Number of models: 1 Model: "" Number of chains: 10 Chain: "B" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2509 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 307} Chain: "E" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2509 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 307} Chain: "C" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "D" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 705 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 84} Chain: "A" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1503 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 4, 'TRANS': 182} Chain: "G" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1750 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "H" Number of atoms: 1750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1750 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "F" Number of atoms: 1749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1749 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.93, per 1000 atoms: 0.52 Number of scatterers: 13244 At special positions: 0 Unit cell: (96.416, 119.472, 124.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 67 16.00 P 6 15.00 Mg 2 11.99 O 2542 8.00 N 2218 7.00 C 8409 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.92 Conformation dependent library (CDL) restraints added in 2.7 seconds 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3178 Finding SS restraints... Secondary structure from input PDB file: 74 helices and 13 sheets defined 49.3% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.41 Creating SS restraints... Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 20 through 24 removed outlier: 4.288A pdb=" N ILE B 24 " --> pdb=" O ASP B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 39 Processing helix chain 'B' and resid 56 through 67 Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 86 through 93 Processing helix chain 'B' and resid 117 through 128 Processing helix chain 'B' and resid 140 through 144 Processing helix chain 'B' and resid 145 through 152 Processing helix chain 'B' and resid 162 through 184 Processing helix chain 'B' and resid 189 through 200 removed outlier: 4.005A pdb=" N VAL B 193 " --> pdb=" O ASP B 189 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASN B 200 " --> pdb=" O LEU B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 Processing helix chain 'B' and resid 235 through 245 Processing helix chain 'B' and resid 247 through 258 Proline residue: B 255 - end of helix Processing helix chain 'B' and resid 260 through 274 removed outlier: 4.142A pdb=" N SER B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 294 removed outlier: 3.615A pdb=" N TYR B 294 " --> pdb=" O GLU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 298 Processing helix chain 'B' and resid 302 through 316 Processing helix chain 'E' and resid 26 through 39 Processing helix chain 'E' and resid 56 through 68 Processing helix chain 'E' and resid 80 through 86 Processing helix chain 'E' and resid 86 through 94 Processing helix chain 'E' and resid 114 through 129 removed outlier: 3.585A pdb=" N GLN E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 145 through 152 removed outlier: 3.700A pdb=" N SER E 150 " --> pdb=" O LYS E 146 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG E 151 " --> pdb=" O PRO E 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N CYS E 152 " --> pdb=" O LEU E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 161 through 183 Processing helix chain 'E' and resid 189 through 200 removed outlier: 3.876A pdb=" N VAL E 193 " --> pdb=" O ASP E 189 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA E 194 " --> pdb=" O MET E 190 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASN E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 215 Processing helix chain 'E' and resid 221 through 227 Processing helix chain 'E' and resid 235 through 245 Processing helix chain 'E' and resid 246 through 258 removed outlier: 3.882A pdb=" N ALA E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 260 through 272 Processing helix chain 'E' and resid 273 through 276 removed outlier: 4.249A pdb=" N VAL E 276 " --> pdb=" O TYR E 273 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 273 through 276' Processing helix chain 'E' and resid 277 through 295 removed outlier: 3.952A pdb=" N ILE E 282 " --> pdb=" O PRO E 278 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ARG E 283 " --> pdb=" O GLN E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 315 Processing helix chain 'C' and resid 235 through 245 Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.541A pdb=" N ARG C 251 " --> pdb=" O VAL C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 259 removed outlier: 4.396A pdb=" N ALA C 259 " --> pdb=" O PRO C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 274 removed outlier: 4.065A pdb=" N PHE C 264 " --> pdb=" O ASP C 260 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR C 273 " --> pdb=" O ALA C 269 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N SER C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 295 removed outlier: 4.188A pdb=" N ILE C 282 " --> pdb=" O PRO C 278 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ARG C 283 " --> pdb=" O GLN C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 315 removed outlier: 3.732A pdb=" N GLU C 315 " --> pdb=" O GLN C 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 235 through 245 Processing helix chain 'D' and resid 246 through 258 Proline residue: D 255 - end of helix Processing helix chain 'D' and resid 261 through 275 Processing helix chain 'D' and resid 277 through 294 removed outlier: 4.389A pdb=" N ILE D 282 " --> pdb=" O PRO D 278 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG D 283 " --> pdb=" O GLN D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 316 Processing helix chain 'A' and resid 13 through 19 Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 35 through 49 Processing helix chain 'A' and resid 61 through 70 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 75 through 85 Processing helix chain 'A' and resid 90 through 102 Processing helix chain 'A' and resid 110 through 118 removed outlier: 3.759A pdb=" N LEU A 114 " --> pdb=" O LYS A 110 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 Processing helix chain 'A' and resid 134 through 148 removed outlier: 3.630A pdb=" N LYS A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 159 removed outlier: 3.944A pdb=" N GLU A 157 " --> pdb=" O LEU A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 162 No H-bonds generated for 'chain 'A' and resid 160 through 162' Processing helix chain 'A' and resid 165 through 171 removed outlier: 4.157A pdb=" N GLU A 169 " --> pdb=" O ASP A 165 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N VAL A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'G' and resid 4 through 18 Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 119 through 134 Processing helix chain 'G' and resid 185 through 187 No H-bonds generated for 'chain 'G' and resid 185 through 187' Processing helix chain 'H' and resid 4 through 15 Processing helix chain 'H' and resid 56 through 66 Processing helix chain 'H' and resid 96 through 100 Processing helix chain 'H' and resid 119 through 134 Processing helix chain 'F' and resid 1004 through 1015 Processing helix chain 'F' and resid 1056 through 1067 removed outlier: 3.538A pdb=" N LEU F1066 " --> pdb=" O GLY F1062 " (cutoff:3.500A) Processing helix chain 'F' and resid 1096 through 1100 removed outlier: 3.588A pdb=" N VAL F1100 " --> pdb=" O PRO F1097 " (cutoff:3.500A) Processing helix chain 'F' and resid 1119 through 1134 removed outlier: 3.506A pdb=" N ARG F1131 " --> pdb=" O LEU F1127 " (cutoff:3.500A) Processing helix chain 'F' and resid 1185 through 1187 No H-bonds generated for 'chain 'F' and resid 1185 through 1187' Processing sheet with id=AA1, first strand: chain 'B' and resid 70 through 75 removed outlier: 6.568A pdb=" N LYS B 102 " --> pdb=" O SER B 133 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N ILE B 135 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 104 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N THR B 137 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE B 106 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'G' and resid 26 through 32 removed outlier: 6.156A pdb=" N GLN G 27 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU G 41 " --> pdb=" O ASN G 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AA5, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AA6, first strand: chain 'G' and resid 142 through 143 removed outlier: 7.138A pdb=" N ILE G 147 " --> pdb=" O LEU G 169 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N LYS G 164 " --> pdb=" O PHE F1091 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 178 through 179 Processing sheet with id=AA8, first strand: chain 'H' and resid 21 through 23 Processing sheet with id=AA9, first strand: chain 'H' and resid 26 through 32 removed outlier: 5.264A pdb=" N GLN H 27 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LYS H 208 " --> pdb=" O LEU H 197 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 73 through 75 removed outlier: 6.578A pdb=" N ILE F1147 " --> pdb=" O LEU F1169 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N PHE F1180 " --> pdb=" O ILE F1140 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 168 through 171 removed outlier: 6.343A pdb=" N THR H 168 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ILE H 149 " --> pdb=" O THR H 168 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY H 170 " --> pdb=" O ILE H 147 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE H 180 " --> pdb=" O ILE H 140 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL H 142 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N PHE H 178 " --> pdb=" O VAL H 142 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 1021 through 1023 Processing sheet with id=AB4, first strand: chain 'F' and resid 1026 through 1032 removed outlier: 5.939A pdb=" N GLN F1027 " --> pdb=" O ILE F1044 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU F1041 " --> pdb=" O ASN F1215 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU F1210 " --> pdb=" O LYS F1195 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA F1114 " --> pdb=" O LEU F1198 " (cutoff:3.500A) 656 hydrogen bonds defined for protein. 1845 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: 3.99 Time building geometry restraints manager: 6.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.37: 4386 1.37 - 1.51: 3754 1.51 - 1.66: 5225 1.66 - 1.80: 84 1.80 - 1.95: 30 Bond restraints: 13479 Sorted by residual: bond pdb=" N ASN A 48 " pdb=" CA ASN A 48 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.20e-02 6.94e+03 1.27e+01 bond pdb=" N ASN B 300 " pdb=" CA ASN B 300 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.17e-02 7.31e+03 7.50e+00 bond pdb=" N HIS C 304 " pdb=" CA HIS C 304 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.19e-02 7.06e+03 7.18e+00 bond pdb=" N TYR G 39 " pdb=" CA TYR G 39 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.21e-02 6.83e+03 6.55e+00 bond pdb=" N LEU H 126 " pdb=" CA LEU H 126 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.20e+00 ... (remaining 13474 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.98: 329 106.98 - 113.80: 7764 113.80 - 120.62: 5437 120.62 - 127.43: 4595 127.43 - 134.25: 110 Bond angle restraints: 18235 Sorted by residual: angle pdb=" N ALA A 56 " pdb=" CA ALA A 56 " pdb=" C ALA A 56 " ideal model delta sigma weight residual 113.43 108.71 4.72 1.26e+00 6.30e-01 1.40e+01 angle pdb=" N ASN A 48 " pdb=" CA ASN A 48 " pdb=" C ASN A 48 " ideal model delta sigma weight residual 111.14 115.01 -3.87 1.08e+00 8.57e-01 1.28e+01 angle pdb=" CA ASN A 48 " pdb=" C ASN A 48 " pdb=" O ASN A 48 " ideal model delta sigma weight residual 120.70 117.31 3.39 1.03e+00 9.43e-01 1.08e+01 angle pdb=" N ASN C 292 " pdb=" CA ASN C 292 " pdb=" C ASN C 292 " ideal model delta sigma weight residual 111.28 107.74 3.54 1.09e+00 8.42e-01 1.06e+01 angle pdb=" CA GLN C 317 " pdb=" C GLN C 317 " pdb=" O GLN C 317 " ideal model delta sigma weight residual 122.41 118.54 3.87 1.21e+00 6.83e-01 1.02e+01 ... (remaining 18230 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7032 17.78 - 35.55: 902 35.55 - 53.33: 201 53.33 - 71.10: 34 71.10 - 88.88: 19 Dihedral angle restraints: 8188 sinusoidal: 3280 harmonic: 4908 Sorted by residual: dihedral pdb=" CA LEU A 10 " pdb=" C LEU A 10 " pdb=" N ASN A 11 " pdb=" CA ASN A 11 " ideal model delta harmonic sigma weight residual 180.00 -163.05 -16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA ASP G 157 " pdb=" CB ASP G 157 " pdb=" CG ASP G 157 " pdb=" OD1 ASP G 157 " ideal model delta sinusoidal sigma weight residual -30.00 -85.78 55.78 1 2.00e+01 2.50e-03 1.05e+01 dihedral pdb=" CB GLU B 108 " pdb=" CG GLU B 108 " pdb=" CD GLU B 108 " pdb=" OE1 GLU B 108 " ideal model delta sinusoidal sigma weight residual 0.00 88.77 -88.77 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 8185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1421 0.035 - 0.069: 443 0.069 - 0.104: 145 0.104 - 0.138: 69 0.138 - 0.173: 3 Chirality restraints: 2081 Sorted by residual: chirality pdb=" CA MET C 316 " pdb=" N MET C 316 " pdb=" C MET C 316 " pdb=" CB MET C 316 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.49e-01 chirality pdb=" CA ILE B 42 " pdb=" N ILE B 42 " pdb=" C ILE B 42 " pdb=" CB ILE B 42 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA GLN C 317 " pdb=" N GLN C 317 " pdb=" C GLN C 317 " pdb=" CB GLN C 317 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 2078 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA D 254 " 0.051 5.00e-02 4.00e+02 7.69e-02 9.45e+00 pdb=" N PRO D 255 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO D 255 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO D 255 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS H 164 " 0.009 2.00e-02 2.50e+03 1.80e-02 3.24e+00 pdb=" C LYS H 164 " -0.031 2.00e-02 2.50e+03 pdb=" O LYS H 164 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR H 165 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 47 " -0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C ILE A 47 " 0.029 2.00e-02 2.50e+03 pdb=" O ILE A 47 " -0.011 2.00e-02 2.50e+03 pdb=" N ASN A 48 " -0.010 2.00e-02 2.50e+03 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 174 2.56 - 3.14: 11778 3.14 - 3.73: 20612 3.73 - 4.31: 29266 4.31 - 4.90: 50016 Nonbonded interactions: 111846 Sorted by model distance: nonbonded pdb=" O2B AGS E 401 " pdb="MG MG E 402 " model vdw 1.974 2.170 nonbonded pdb=" NZ LYS B 56 " pdb="MG MG B 402 " model vdw 2.102 2.250 nonbonded pdb=" O ASN B 300 " pdb=" OG1 THR B 301 " model vdw 2.148 2.440 nonbonded pdb=" N GLU F1175 " pdb=" OE1 GLU F1175 " model vdw 2.170 2.520 nonbonded pdb=" O2B AGS E 401 " pdb=" O2G AGS E 401 " model vdw 2.195 2.440 ... (remaining 111841 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'F' selection = (chain 'G' and (resid 1 through 227 or (resid 228 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )))) selection = (chain 'H' and (resid 1 through 227 or (resid 228 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )))) } 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: 0.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 38.390 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 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 0.043 13479 Z= 0.226 Angle : 0.480 5.604 18235 Z= 0.291 Chirality : 0.041 0.173 2081 Planarity : 0.003 0.077 2327 Dihedral : 16.689 88.879 5010 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 46.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.28 % Favored : 94.48 % Rotamer: Outliers : 0.49 % Allowed : 22.80 % Favored : 76.71 % 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: 0.09 (0.22), residues: 1667 helix: 1.56 (0.20), residues: 698 sheet: -1.52 (0.31), residues: 309 loop : -0.69 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 263 HIS 0.014 0.001 HIS D 304 PHE 0.027 0.001 PHE B 109 TYR 0.011 0.001 TYR D 261 ARG 0.002 0.000 ARG E 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 229 time to evaluate : 1.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 97 PHE cc_start: 0.7857 (t80) cc_final: 0.7652 (t80) REVERT: B 142 ASP cc_start: 0.8768 (m-30) cc_final: 0.8534 (p0) REVERT: B 168 MET cc_start: 0.9449 (ttp) cc_final: 0.9137 (ptm) REVERT: B 169 MET cc_start: 0.9077 (mmm) cc_final: 0.8784 (mmm) REVERT: B 172 MET cc_start: 0.9456 (tpt) cc_final: 0.8856 (tpt) REVERT: B 182 HIS cc_start: 0.8834 (m90) cc_final: 0.8550 (m90) REVERT: B 261 TYR cc_start: 0.7879 (t80) cc_final: 0.7637 (t80) REVERT: B 284 MET cc_start: 0.9677 (tmm) cc_final: 0.9388 (tmm) REVERT: B 294 TYR cc_start: 0.9300 (m-80) cc_final: 0.9044 (m-80) REVERT: B 307 TYR cc_start: 0.9052 (t80) cc_final: 0.8683 (t80) REVERT: E 169 MET cc_start: 0.9463 (mtt) cc_final: 0.9079 (mtp) REVERT: E 172 MET cc_start: 0.9331 (tpt) cc_final: 0.9109 (tpt) REVERT: E 284 MET cc_start: 0.9647 (tmm) cc_final: 0.9330 (tmm) REVERT: C 302 GLU cc_start: 0.9224 (pt0) cc_final: 0.8845 (pm20) REVERT: C 317 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.6946 (tp40) REVERT: D 244 ASN cc_start: 0.8730 (m110) cc_final: 0.8490 (m-40) REVERT: D 249 GLN cc_start: 0.9332 (tp40) cc_final: 0.9043 (tp-100) REVERT: D 291 ASN cc_start: 0.8666 (t0) cc_final: 0.8282 (t0) REVERT: A 4 PHE cc_start: 0.8107 (m-80) cc_final: 0.7808 (m-80) REVERT: A 21 ASP cc_start: 0.8466 (t0) cc_final: 0.7949 (t0) REVERT: A 30 ASP cc_start: 0.8947 (m-30) cc_final: 0.8716 (m-30) REVERT: A 156 LYS cc_start: 0.9599 (tmtt) cc_final: 0.9334 (tppt) REVERT: G 32 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8327 (ptm-80) REVERT: H 126 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9240 (tp) REVERT: H 134 GLN cc_start: 0.9233 (mm-40) cc_final: 0.8884 (mm-40) REVERT: F 1055 TYR cc_start: 0.8109 (p90) cc_final: 0.7524 (p90) REVERT: F 1128 ARG cc_start: 0.9108 (mpp80) cc_final: 0.8859 (mtp85) REVERT: F 1134 GLN cc_start: 0.8878 (mp10) cc_final: 0.8674 (mp10) outliers start: 7 outliers final: 2 residues processed: 233 average time/residue: 0.2541 time to fit residues: 85.9973 Evaluate side-chains 184 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 180 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain C residue 316 MET Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain H residue 126 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 0.9980 chunk 122 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 126 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 94 optimal weight: 0.3980 chunk 147 optimal weight: 8.9990 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 139 ASN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 48 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 ASN ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN H 13 ASN H 153 ASN H 176 ASN F1179 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13479 Z= 0.265 Angle : 0.655 9.466 18235 Z= 0.340 Chirality : 0.045 0.192 2081 Planarity : 0.004 0.056 2327 Dihedral : 6.828 72.169 1840 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.50 % Favored : 95.26 % Rotamer: Outliers : 3.71 % Allowed : 20.70 % Favored : 75.59 % 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: -0.20 (0.21), residues: 1667 helix: 1.15 (0.19), residues: 726 sheet: -1.69 (0.28), residues: 311 loop : -0.68 (0.25), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 318 HIS 0.013 0.002 HIS D 304 PHE 0.026 0.002 PHE B 109 TYR 0.028 0.002 TYR C 307 ARG 0.004 0.001 ARG H 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 206 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7791 (ppp) cc_final: 0.7450 (ppp) REVERT: B 97 PHE cc_start: 0.7864 (t80) cc_final: 0.7649 (t80) REVERT: B 106 ILE cc_start: 0.9238 (OUTLIER) cc_final: 0.9013 (mm) REVERT: B 120 HIS cc_start: 0.9052 (OUTLIER) cc_final: 0.8714 (m90) REVERT: B 142 ASP cc_start: 0.8760 (m-30) cc_final: 0.8493 (p0) REVERT: B 169 MET cc_start: 0.9224 (OUTLIER) cc_final: 0.8972 (mmt) REVERT: B 172 MET cc_start: 0.9436 (tpt) cc_final: 0.8920 (tpt) REVERT: B 182 HIS cc_start: 0.8817 (m90) cc_final: 0.8462 (m90) REVERT: B 281 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9059 (tt) REVERT: B 284 MET cc_start: 0.9661 (tmm) cc_final: 0.9267 (tmm) REVERT: B 307 TYR cc_start: 0.9153 (t80) cc_final: 0.8795 (t80) REVERT: E 98 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8499 (p0) REVERT: E 120 HIS cc_start: 0.8605 (m170) cc_final: 0.8341 (m170) REVERT: E 137 THR cc_start: 0.9240 (OUTLIER) cc_final: 0.8472 (p) REVERT: E 169 MET cc_start: 0.9453 (mtt) cc_final: 0.9218 (mtp) REVERT: E 284 MET cc_start: 0.9598 (tmm) cc_final: 0.9227 (tmm) REVERT: E 316 MET cc_start: 0.9160 (mmp) cc_final: 0.8834 (mmm) REVERT: C 302 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8827 (pm20) REVERT: C 305 LEU cc_start: 0.9430 (mm) cc_final: 0.9082 (mp) REVERT: D 244 ASN cc_start: 0.8731 (m110) cc_final: 0.8418 (m-40) REVERT: D 249 GLN cc_start: 0.9524 (tp40) cc_final: 0.9209 (tp-100) REVERT: D 291 ASN cc_start: 0.8740 (t0) cc_final: 0.8435 (t0) REVERT: A 4 PHE cc_start: 0.8361 (m-80) cc_final: 0.8013 (m-80) REVERT: A 21 ASP cc_start: 0.8835 (t0) cc_final: 0.8480 (t0) REVERT: A 30 ASP cc_start: 0.9015 (m-30) cc_final: 0.8804 (m-30) REVERT: A 63 PHE cc_start: 0.8970 (t80) cc_final: 0.8748 (t80) REVERT: A 99 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8181 (tpt) REVERT: A 156 LYS cc_start: 0.9594 (tmtt) cc_final: 0.9327 (tppt) REVERT: G 32 ARG cc_start: 0.8579 (ttp80) cc_final: 0.8000 (ttt-90) REVERT: H 172 TYR cc_start: 0.8980 (t80) cc_final: 0.8744 (t80) REVERT: H 197 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8699 (pp) REVERT: F 1055 TYR cc_start: 0.8050 (p90) cc_final: 0.7622 (p90) outliers start: 53 outliers final: 19 residues processed: 246 average time/residue: 0.2374 time to fit residues: 86.6938 Evaluate side-chains 207 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 57 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 124 GLN Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1223 ASP Chi-restraints excluded: chain F residue 1224 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 40 optimal weight: 7.9990 chunk 147 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 101 GLN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 179 ASN ** F1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 13479 Z= 0.437 Angle : 0.665 9.199 18235 Z= 0.349 Chirality : 0.045 0.310 2081 Planarity : 0.004 0.100 2327 Dihedral : 6.649 69.367 1832 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 17.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.50 % Favored : 95.26 % Rotamer: Outliers : 4.41 % Allowed : 22.31 % Favored : 73.29 % 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: -0.36 (0.21), residues: 1667 helix: 1.00 (0.19), residues: 728 sheet: -1.67 (0.28), residues: 330 loop : -0.77 (0.26), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 318 HIS 0.010 0.002 HIS D 304 PHE 0.019 0.002 PHE B 109 TYR 0.017 0.002 TYR A 60 ARG 0.004 0.001 ARG H 162 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 184 time to evaluate : 1.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.7973 (ppp) cc_final: 0.7601 (ppp) REVERT: B 97 PHE cc_start: 0.7926 (t80) cc_final: 0.7696 (t80) REVERT: B 120 HIS cc_start: 0.9255 (OUTLIER) cc_final: 0.8688 (m90) REVERT: B 142 ASP cc_start: 0.8811 (m-30) cc_final: 0.8539 (p0) REVERT: B 172 MET cc_start: 0.9472 (tpt) cc_final: 0.8901 (tpt) REVERT: B 182 HIS cc_start: 0.8797 (m90) cc_final: 0.8434 (m90) REVERT: B 261 TYR cc_start: 0.7395 (t80) cc_final: 0.7140 (t80) REVERT: B 281 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.8930 (tt) REVERT: B 284 MET cc_start: 0.9662 (tmm) cc_final: 0.9140 (tmm) REVERT: B 285 TYR cc_start: 0.9418 (m-80) cc_final: 0.8973 (m-80) REVERT: B 307 TYR cc_start: 0.9140 (t80) cc_final: 0.8842 (t80) REVERT: E 98 ASP cc_start: 0.9001 (OUTLIER) cc_final: 0.8478 (p0) REVERT: E 120 HIS cc_start: 0.8770 (m170) cc_final: 0.8519 (m170) REVERT: E 137 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8523 (p) REVERT: E 169 MET cc_start: 0.9478 (mtt) cc_final: 0.9262 (mtp) REVERT: E 240 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8725 (pp20) REVERT: E 284 MET cc_start: 0.9636 (tmm) cc_final: 0.9258 (tmm) REVERT: E 316 MET cc_start: 0.9279 (OUTLIER) cc_final: 0.8923 (mmm) REVERT: C 302 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8949 (pm20) REVERT: C 305 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9195 (mp) REVERT: C 307 TYR cc_start: 0.9316 (t80) cc_final: 0.9059 (t80) REVERT: D 244 ASN cc_start: 0.8755 (m110) cc_final: 0.8431 (m-40) REVERT: D 249 GLN cc_start: 0.9575 (tp40) cc_final: 0.9337 (tp-100) REVERT: D 261 TYR cc_start: 0.8737 (t80) cc_final: 0.8531 (t80) REVERT: D 284 MET cc_start: 0.9402 (tmm) cc_final: 0.8784 (tmm) REVERT: D 291 ASN cc_start: 0.8840 (t0) cc_final: 0.8582 (t0) REVERT: A 4 PHE cc_start: 0.8473 (m-80) cc_final: 0.8124 (m-80) REVERT: A 21 ASP cc_start: 0.8894 (t0) cc_final: 0.8553 (t0) REVERT: A 117 ASP cc_start: 0.8831 (t0) cc_final: 0.8531 (t0) REVERT: A 168 LYS cc_start: 0.9153 (mmmt) cc_final: 0.8614 (mmmt) REVERT: A 172 LYS cc_start: 0.9242 (mppt) cc_final: 0.8964 (mmtm) REVERT: G 32 ARG cc_start: 0.8720 (ttp80) cc_final: 0.8105 (ttt-90) REVERT: G 51 ASP cc_start: 0.8896 (OUTLIER) cc_final: 0.8589 (m-30) REVERT: G 134 GLN cc_start: 0.9086 (mm-40) cc_final: 0.8883 (mm-40) REVERT: F 1055 TYR cc_start: 0.8178 (p90) cc_final: 0.7800 (p90) outliers start: 63 outliers final: 34 residues processed: 227 average time/residue: 0.2369 time to fit residues: 79.0380 Evaluate side-chains 214 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1223 ASP Chi-restraints excluded: chain F residue 1224 SER Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 145 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 98 optimal weight: 5.9990 chunk 147 optimal weight: 0.9990 chunk 156 optimal weight: 6.9990 chunk 77 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13479 Z= 0.233 Angle : 0.597 10.084 18235 Z= 0.306 Chirality : 0.044 0.320 2081 Planarity : 0.003 0.043 2327 Dihedral : 6.511 63.958 1832 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.32 % Favored : 95.44 % Rotamer: Outliers : 3.85 % Allowed : 23.78 % Favored : 72.38 % 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: -0.23 (0.21), residues: 1667 helix: 1.14 (0.19), residues: 730 sheet: -1.58 (0.28), residues: 314 loop : -0.81 (0.25), residues: 623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 263 HIS 0.008 0.001 HIS D 304 PHE 0.016 0.002 PHE E 264 TYR 0.031 0.002 TYR B 214 ARG 0.006 0.000 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 193 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8147 (ppp) cc_final: 0.7851 (ppp) REVERT: B 13 GLN cc_start: 0.9827 (OUTLIER) cc_final: 0.9255 (mp10) REVERT: B 120 HIS cc_start: 0.9083 (OUTLIER) cc_final: 0.8670 (m90) REVERT: B 169 MET cc_start: 0.9323 (mmt) cc_final: 0.8998 (mmt) REVERT: B 172 MET cc_start: 0.9435 (tpt) cc_final: 0.8880 (tpt) REVERT: B 182 HIS cc_start: 0.8760 (m90) cc_final: 0.8371 (m90) REVERT: B 190 MET cc_start: 0.9231 (tpt) cc_final: 0.9019 (tpp) REVERT: B 281 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.8885 (tt) REVERT: B 284 MET cc_start: 0.9673 (tmm) cc_final: 0.9162 (tmm) REVERT: B 307 TYR cc_start: 0.9095 (t80) cc_final: 0.8662 (t80) REVERT: E 98 ASP cc_start: 0.9019 (OUTLIER) cc_final: 0.8476 (p0) REVERT: E 120 HIS cc_start: 0.8695 (m170) cc_final: 0.8410 (m170) REVERT: E 137 THR cc_start: 0.9218 (OUTLIER) cc_final: 0.8396 (p) REVERT: E 169 MET cc_start: 0.9469 (mtt) cc_final: 0.9263 (mtp) REVERT: E 240 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8726 (tm-30) REVERT: E 284 MET cc_start: 0.9649 (tmm) cc_final: 0.9362 (tmm) REVERT: E 316 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8877 (mmm) REVERT: C 302 GLU cc_start: 0.9177 (OUTLIER) cc_final: 0.8918 (pm20) REVERT: C 305 LEU cc_start: 0.9565 (OUTLIER) cc_final: 0.9232 (mp) REVERT: D 244 ASN cc_start: 0.8742 (m110) cc_final: 0.8407 (m-40) REVERT: D 249 GLN cc_start: 0.9608 (tp40) cc_final: 0.9365 (tp-100) REVERT: D 253 LEU cc_start: 0.9432 (pp) cc_final: 0.9065 (pp) REVERT: D 284 MET cc_start: 0.9477 (tmm) cc_final: 0.8852 (tmm) REVERT: D 291 ASN cc_start: 0.8800 (t0) cc_final: 0.8574 (t0) REVERT: A 4 PHE cc_start: 0.8454 (m-80) cc_final: 0.8049 (m-80) REVERT: A 21 ASP cc_start: 0.8943 (t0) cc_final: 0.8613 (t0) REVERT: A 99 MET cc_start: 0.8778 (mmm) cc_final: 0.8256 (tpt) REVERT: A 168 LYS cc_start: 0.9180 (mmmt) cc_final: 0.8574 (mmmt) REVERT: A 172 LYS cc_start: 0.9222 (mppt) cc_final: 0.8928 (mmtm) REVERT: G 32 ARG cc_start: 0.8719 (ttp80) cc_final: 0.8514 (ptm-80) REVERT: H 117 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8569 (tm-30) REVERT: H 172 TYR cc_start: 0.8863 (t80) cc_final: 0.8597 (t80) REVERT: F 1055 TYR cc_start: 0.8002 (p90) cc_final: 0.7572 (p90) outliers start: 55 outliers final: 33 residues processed: 233 average time/residue: 0.2402 time to fit residues: 82.7509 Evaluate side-chains 214 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 99 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 130 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 2 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 64 optimal weight: 10.0000 chunk 133 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 79 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13479 Z= 0.315 Angle : 0.614 9.660 18235 Z= 0.314 Chirality : 0.044 0.267 2081 Planarity : 0.003 0.038 2327 Dihedral : 6.519 61.214 1832 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.68 % Favored : 95.08 % Rotamer: Outliers : 4.20 % Allowed : 24.41 % Favored : 71.40 % 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: -0.15 (0.21), residues: 1667 helix: 1.19 (0.19), residues: 731 sheet: -1.48 (0.29), residues: 320 loop : -0.77 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 263 HIS 0.006 0.001 HIS D 304 PHE 0.017 0.002 PHE E 264 TYR 0.026 0.002 TYR B 214 ARG 0.006 0.001 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 183 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 71 MET cc_start: 0.8681 (tmm) cc_final: 0.8440 (tmm) REVERT: B 106 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8927 (mm) REVERT: B 120 HIS cc_start: 0.9141 (OUTLIER) cc_final: 0.8657 (m90) REVERT: B 169 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8849 (mmt) REVERT: B 172 MET cc_start: 0.9425 (tpt) cc_final: 0.8893 (tpt) REVERT: B 182 HIS cc_start: 0.8777 (m90) cc_final: 0.8370 (m90) REVERT: B 281 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9028 (tt) REVERT: B 284 MET cc_start: 0.9675 (tmm) cc_final: 0.9225 (tmm) REVERT: B 307 TYR cc_start: 0.9145 (t80) cc_final: 0.8689 (t80) REVERT: E 98 ASP cc_start: 0.9042 (OUTLIER) cc_final: 0.8480 (p0) REVERT: E 137 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8436 (p) REVERT: E 240 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8671 (pp20) REVERT: E 284 MET cc_start: 0.9651 (tmm) cc_final: 0.9359 (tmm) REVERT: E 293 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8958 (tt0) REVERT: E 316 MET cc_start: 0.9235 (OUTLIER) cc_final: 0.8915 (mmm) REVERT: C 302 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8907 (pm20) REVERT: C 305 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9303 (mp) REVERT: D 244 ASN cc_start: 0.8776 (m110) cc_final: 0.8450 (m-40) REVERT: D 249 GLN cc_start: 0.9610 (tp40) cc_final: 0.9407 (tp-100) REVERT: D 253 LEU cc_start: 0.9420 (pp) cc_final: 0.9096 (pp) REVERT: D 284 MET cc_start: 0.9548 (tmm) cc_final: 0.8912 (tmm) REVERT: A 4 PHE cc_start: 0.8514 (m-80) cc_final: 0.8059 (m-80) REVERT: A 21 ASP cc_start: 0.8969 (t0) cc_final: 0.8659 (t0) REVERT: A 75 CYS cc_start: 0.9615 (OUTLIER) cc_final: 0.9375 (p) REVERT: A 99 MET cc_start: 0.8784 (mmm) cc_final: 0.8275 (tpt) REVERT: A 117 ASP cc_start: 0.8870 (t0) cc_final: 0.8425 (t0) REVERT: A 168 LYS cc_start: 0.9203 (mmmt) cc_final: 0.8550 (mmmt) REVERT: A 172 LYS cc_start: 0.9234 (mppt) cc_final: 0.8921 (mmtm) REVERT: G 32 ARG cc_start: 0.8740 (ttp80) cc_final: 0.8125 (ttt-90) REVERT: G 137 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8833 (p) REVERT: H 8 THR cc_start: 0.9474 (OUTLIER) cc_final: 0.9216 (p) REVERT: H 117 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8601 (tm-30) REVERT: H 172 TYR cc_start: 0.9015 (t80) cc_final: 0.8531 (t80) REVERT: F 1055 TYR cc_start: 0.8112 (p90) cc_final: 0.7692 (p90) outliers start: 60 outliers final: 38 residues processed: 228 average time/residue: 0.2353 time to fit residues: 79.5124 Evaluate side-chains 228 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 175 time to evaluate : 1.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 187 ILE Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 221 ASP Chi-restraints excluded: chain E residue 240 GLU Chi-restraints excluded: chain E residue 293 GLN Chi-restraints excluded: chain E residue 316 MET Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 73 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 141 THR Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain H residue 189 MET Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1223 ASP Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 52 optimal weight: 10.0000 chunk 141 optimal weight: 0.0970 chunk 30 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 38 optimal weight: 0.6980 chunk 156 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13479 Z= 0.168 Angle : 0.606 11.864 18235 Z= 0.301 Chirality : 0.043 0.319 2081 Planarity : 0.003 0.038 2327 Dihedral : 6.400 59.898 1832 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.78 % Favored : 96.04 % Rotamer: Outliers : 3.78 % Allowed : 24.69 % Favored : 71.54 % 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: -0.13 (0.21), residues: 1667 helix: 1.18 (0.19), residues: 734 sheet: -1.47 (0.29), residues: 313 loop : -0.75 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 263 HIS 0.013 0.001 HIS D 304 PHE 0.014 0.001 PHE E 264 TYR 0.021 0.002 TYR C 307 ARG 0.007 0.001 ARG G 162 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 200 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.9825 (OUTLIER) cc_final: 0.9244 (mp10) REVERT: B 106 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8919 (mm) REVERT: B 120 HIS cc_start: 0.8891 (OUTLIER) cc_final: 0.8587 (m90) REVERT: B 169 MET cc_start: 0.9261 (OUTLIER) cc_final: 0.8854 (mmt) REVERT: B 172 MET cc_start: 0.9414 (tpt) cc_final: 0.8896 (tpt) REVERT: B 182 HIS cc_start: 0.8713 (m90) cc_final: 0.8360 (m-70) REVERT: B 281 ILE cc_start: 0.9302 (OUTLIER) cc_final: 0.9008 (tt) REVERT: B 284 MET cc_start: 0.9682 (tmm) cc_final: 0.9277 (tmm) REVERT: B 307 TYR cc_start: 0.8974 (t80) cc_final: 0.8618 (t80) REVERT: E 98 ASP cc_start: 0.9023 (OUTLIER) cc_final: 0.8518 (p0) REVERT: E 120 HIS cc_start: 0.8661 (m170) cc_final: 0.8358 (m170) REVERT: E 137 THR cc_start: 0.9175 (OUTLIER) cc_final: 0.8334 (p) REVERT: E 168 MET cc_start: 0.8855 (mtt) cc_final: 0.8443 (mtt) REVERT: E 284 MET cc_start: 0.9646 (tmm) cc_final: 0.9410 (tmm) REVERT: C 276 VAL cc_start: 0.8935 (t) cc_final: 0.8699 (t) REVERT: C 279 GLN cc_start: 0.8932 (pp30) cc_final: 0.8654 (pp30) REVERT: C 302 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.8940 (pm20) REVERT: C 305 LEU cc_start: 0.9577 (OUTLIER) cc_final: 0.9231 (mt) REVERT: D 244 ASN cc_start: 0.8745 (m110) cc_final: 0.8409 (m-40) REVERT: D 249 GLN cc_start: 0.9602 (tp40) cc_final: 0.9393 (tp-100) REVERT: D 253 LEU cc_start: 0.9352 (pp) cc_final: 0.9078 (pp) REVERT: D 284 MET cc_start: 0.9554 (tmm) cc_final: 0.8899 (tmm) REVERT: A 4 PHE cc_start: 0.8448 (m-80) cc_final: 0.7972 (m-80) REVERT: A 21 ASP cc_start: 0.8950 (t0) cc_final: 0.8650 (t0) REVERT: A 75 CYS cc_start: 0.9626 (OUTLIER) cc_final: 0.9364 (p) REVERT: A 99 MET cc_start: 0.8689 (OUTLIER) cc_final: 0.8206 (tpt) REVERT: A 168 LYS cc_start: 0.9215 (mmmt) cc_final: 0.8594 (mmmt) REVERT: A 172 LYS cc_start: 0.9221 (mppt) cc_final: 0.8903 (mmtm) REVERT: G 27 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8447 (mt0) REVERT: G 32 ARG cc_start: 0.8685 (ttp80) cc_final: 0.8159 (ttt-90) REVERT: G 37 THR cc_start: 0.9654 (OUTLIER) cc_final: 0.9433 (p) REVERT: H 8 THR cc_start: 0.9456 (OUTLIER) cc_final: 0.9191 (p) REVERT: H 117 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8647 (tm-30) REVERT: H 162 ARG cc_start: 0.8639 (ttm110) cc_final: 0.8112 (ptp-110) REVERT: H 172 TYR cc_start: 0.8992 (t80) cc_final: 0.8544 (t80) REVERT: F 1027 GLN cc_start: 0.8967 (mt0) cc_final: 0.8625 (mt0) REVERT: F 1055 TYR cc_start: 0.7940 (p90) cc_final: 0.7548 (p90) REVERT: F 1163 VAL cc_start: 0.9334 (OUTLIER) cc_final: 0.9063 (t) outliers start: 54 outliers final: 26 residues processed: 239 average time/residue: 0.2544 time to fit residues: 90.1593 Evaluate side-chains 221 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 179 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 131 ASN Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 27 GLN Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 151 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 89 optimal weight: 10.0000 chunk 114 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 131 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 156 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13479 Z= 0.249 Angle : 0.636 12.204 18235 Z= 0.313 Chirality : 0.044 0.335 2081 Planarity : 0.003 0.048 2327 Dihedral : 6.352 58.910 1832 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.62 % Favored : 95.20 % Rotamer: Outliers : 4.48 % Allowed : 24.76 % Favored : 70.77 % 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: -0.02 (0.21), residues: 1667 helix: 1.25 (0.19), residues: 733 sheet: -1.29 (0.28), residues: 321 loop : -0.70 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 263 HIS 0.015 0.001 HIS B 295 PHE 0.018 0.001 PHE A 63 TYR 0.019 0.002 TYR B 294 ARG 0.014 0.001 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 186 time to evaluate : 1.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.9825 (OUTLIER) cc_final: 0.9239 (mp10) REVERT: B 106 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8884 (mm) REVERT: B 120 HIS cc_start: 0.8996 (OUTLIER) cc_final: 0.8600 (m90) REVERT: B 169 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8863 (mmt) REVERT: B 172 MET cc_start: 0.9414 (tpt) cc_final: 0.8874 (tpt) REVERT: B 182 HIS cc_start: 0.8713 (m90) cc_final: 0.8357 (m-70) REVERT: B 284 MET cc_start: 0.9696 (tmm) cc_final: 0.9271 (tmm) REVERT: B 307 TYR cc_start: 0.9000 (t80) cc_final: 0.8640 (t80) REVERT: E 98 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8514 (p0) REVERT: E 137 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8381 (p) REVERT: E 168 MET cc_start: 0.8880 (mtt) cc_final: 0.8405 (mtt) REVERT: E 190 MET cc_start: 0.9511 (tpp) cc_final: 0.9272 (tpp) REVERT: E 284 MET cc_start: 0.9667 (tmm) cc_final: 0.9444 (tmm) REVERT: C 279 GLN cc_start: 0.8924 (pp30) cc_final: 0.8671 (pp30) REVERT: C 302 GLU cc_start: 0.9171 (OUTLIER) cc_final: 0.8941 (pm20) REVERT: C 305 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9316 (mp) REVERT: D 244 ASN cc_start: 0.8773 (m110) cc_final: 0.8421 (m-40) REVERT: D 253 LEU cc_start: 0.9384 (pp) cc_final: 0.9104 (pp) REVERT: D 270 GLU cc_start: 0.9119 (mt-10) cc_final: 0.8851 (pt0) REVERT: D 284 MET cc_start: 0.9546 (tmm) cc_final: 0.8884 (tmm) REVERT: A 4 PHE cc_start: 0.8465 (m-80) cc_final: 0.8012 (m-80) REVERT: A 21 ASP cc_start: 0.8997 (t0) cc_final: 0.8673 (t0) REVERT: A 47 ILE cc_start: 0.9550 (mt) cc_final: 0.9304 (mm) REVERT: A 75 CYS cc_start: 0.9624 (OUTLIER) cc_final: 0.9371 (p) REVERT: A 99 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.8064 (tpt) REVERT: A 117 ASP cc_start: 0.8848 (t0) cc_final: 0.8361 (t0) REVERT: A 168 LYS cc_start: 0.9218 (mmmt) cc_final: 0.8813 (mmmt) REVERT: A 171 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8680 (t) REVERT: A 172 LYS cc_start: 0.9232 (mppt) cc_final: 0.8945 (mmtm) REVERT: G 32 ARG cc_start: 0.8729 (ttp80) cc_final: 0.8517 (ptm-80) REVERT: G 37 THR cc_start: 0.9659 (OUTLIER) cc_final: 0.9456 (p) REVERT: G 134 GLN cc_start: 0.8538 (mp10) cc_final: 0.8323 (mp10) REVERT: G 137 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8775 (p) REVERT: H 117 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8653 (tm-30) REVERT: H 162 ARG cc_start: 0.8654 (ttm110) cc_final: 0.8193 (ptp-110) REVERT: H 172 TYR cc_start: 0.9050 (t80) cc_final: 0.8536 (t80) REVERT: F 1027 GLN cc_start: 0.8940 (mt0) cc_final: 0.8584 (mt0) REVERT: F 1055 TYR cc_start: 0.8017 (p90) cc_final: 0.7602 (p90) REVERT: F 1163 VAL cc_start: 0.9341 (OUTLIER) cc_final: 0.9069 (t) outliers start: 64 outliers final: 35 residues processed: 235 average time/residue: 0.2334 time to fit residues: 80.9563 Evaluate side-chains 229 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 179 time to evaluate : 1.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 248 LYS Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1142 VAL Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1223 ASP Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 96 optimal weight: 8.9990 chunk 62 optimal weight: 20.0000 chunk 93 optimal weight: 0.3980 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 122 optimal weight: 9.9990 chunk 142 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 13479 Z= 0.172 Angle : 0.642 14.307 18235 Z= 0.311 Chirality : 0.044 0.377 2081 Planarity : 0.003 0.048 2327 Dihedral : 6.250 58.440 1832 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.08 % Favored : 95.74 % Rotamer: Outliers : 3.92 % Allowed : 25.17 % Favored : 70.91 % 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: 0.06 (0.21), residues: 1667 helix: 1.31 (0.19), residues: 731 sheet: -1.26 (0.28), residues: 319 loop : -0.65 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 263 HIS 0.010 0.001 HIS D 304 PHE 0.015 0.001 PHE G 28 TYR 0.024 0.002 TYR C 307 ARG 0.010 0.001 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 197 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 13 GLN cc_start: 0.9818 (OUTLIER) cc_final: 0.9233 (mp10) REVERT: B 106 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8902 (mm) REVERT: B 120 HIS cc_start: 0.8836 (OUTLIER) cc_final: 0.8614 (m90) REVERT: B 169 MET cc_start: 0.9321 (OUTLIER) cc_final: 0.8960 (mmt) REVERT: B 172 MET cc_start: 0.9403 (tpt) cc_final: 0.8858 (tpt) REVERT: B 182 HIS cc_start: 0.8636 (m90) cc_final: 0.8251 (m-70) REVERT: B 284 MET cc_start: 0.9688 (tmm) cc_final: 0.9314 (tmm) REVERT: B 307 TYR cc_start: 0.8958 (t80) cc_final: 0.8588 (t80) REVERT: E 98 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8529 (p0) REVERT: E 120 HIS cc_start: 0.8535 (m170) cc_final: 0.8325 (m170) REVERT: E 137 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8278 (p) REVERT: E 168 MET cc_start: 0.8794 (mtt) cc_final: 0.8453 (mtt) REVERT: E 284 MET cc_start: 0.9667 (tmm) cc_final: 0.9405 (tmm) REVERT: E 285 TYR cc_start: 0.9066 (OUTLIER) cc_final: 0.7957 (t80) REVERT: E 297 ILE cc_start: 0.8881 (mm) cc_final: 0.8559 (tt) REVERT: C 279 GLN cc_start: 0.8926 (pp30) cc_final: 0.8710 (pp30) REVERT: C 302 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8895 (pm20) REVERT: C 305 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9307 (mt) REVERT: D 244 ASN cc_start: 0.8754 (m110) cc_final: 0.8402 (m-40) REVERT: D 270 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8857 (pt0) REVERT: D 284 MET cc_start: 0.9542 (tmm) cc_final: 0.8891 (tmm) REVERT: A 4 PHE cc_start: 0.8416 (m-80) cc_final: 0.7934 (m-80) REVERT: A 21 ASP cc_start: 0.8949 (t0) cc_final: 0.8664 (t0) REVERT: A 75 CYS cc_start: 0.9636 (OUTLIER) cc_final: 0.9389 (p) REVERT: A 99 MET cc_start: 0.8650 (OUTLIER) cc_final: 0.8220 (mmm) REVERT: A 168 LYS cc_start: 0.9210 (mmmt) cc_final: 0.8818 (mmmt) REVERT: A 171 THR cc_start: 0.8946 (OUTLIER) cc_final: 0.8726 (t) REVERT: A 172 LYS cc_start: 0.9230 (mppt) cc_final: 0.8909 (mmtm) REVERT: G 32 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8152 (ttt-90) REVERT: G 137 THR cc_start: 0.9051 (OUTLIER) cc_final: 0.8699 (p) REVERT: H 8 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9179 (p) REVERT: H 117 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8640 (tm-30) REVERT: H 162 ARG cc_start: 0.8568 (ttm110) cc_final: 0.8136 (ptp-110) REVERT: H 172 TYR cc_start: 0.9027 (t80) cc_final: 0.8525 (t80) REVERT: F 1027 GLN cc_start: 0.8908 (mt0) cc_final: 0.8528 (mt0) REVERT: F 1055 TYR cc_start: 0.7822 (p90) cc_final: 0.7404 (p90) REVERT: F 1163 VAL cc_start: 0.9329 (OUTLIER) cc_final: 0.9101 (t) outliers start: 56 outliers final: 33 residues processed: 236 average time/residue: 0.2381 time to fit residues: 82.2953 Evaluate side-chains 236 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 148 LEU Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 7 ASP Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1051 ASP Chi-restraints excluded: chain F residue 1142 VAL Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1189 MET Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 149 optimal weight: 0.9980 chunk 136 optimal weight: 5.9990 chunk 145 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 131 optimal weight: 8.9990 chunk 137 optimal weight: 5.9990 chunk 144 optimal weight: 0.0980 chunk 95 optimal weight: 9.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN G 13 ASN G 150 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13479 Z= 0.232 Angle : 0.660 14.233 18235 Z= 0.318 Chirality : 0.044 0.361 2081 Planarity : 0.003 0.038 2327 Dihedral : 6.239 58.262 1832 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.62 % Favored : 95.20 % Rotamer: Outliers : 3.85 % Allowed : 25.87 % Favored : 70.28 % 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: 0.16 (0.21), residues: 1667 helix: 1.32 (0.19), residues: 738 sheet: -1.18 (0.29), residues: 321 loop : -0.54 (0.26), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 263 HIS 0.009 0.001 HIS D 304 PHE 0.027 0.001 PHE B 97 TYR 0.032 0.002 TYR C 273 ARG 0.009 0.001 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 186 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8214 (ppp) cc_final: 0.7844 (ppp) REVERT: B 13 GLN cc_start: 0.9819 (OUTLIER) cc_final: 0.9232 (mp10) REVERT: B 106 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8869 (mm) REVERT: B 169 MET cc_start: 0.9315 (OUTLIER) cc_final: 0.8965 (mmt) REVERT: B 182 HIS cc_start: 0.8634 (m90) cc_final: 0.8254 (m-70) REVERT: B 284 MET cc_start: 0.9704 (tmm) cc_final: 0.9325 (tmm) REVERT: B 307 TYR cc_start: 0.9032 (t80) cc_final: 0.8624 (t80) REVERT: E 98 ASP cc_start: 0.9031 (OUTLIER) cc_final: 0.8532 (p0) REVERT: E 120 HIS cc_start: 0.8625 (m170) cc_final: 0.8395 (m170) REVERT: E 137 THR cc_start: 0.9203 (OUTLIER) cc_final: 0.8347 (p) REVERT: E 168 MET cc_start: 0.8873 (mtt) cc_final: 0.8440 (mtt) REVERT: E 285 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8012 (t80) REVERT: E 297 ILE cc_start: 0.8871 (mm) cc_final: 0.8489 (tt) REVERT: C 302 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8918 (pm20) REVERT: C 305 LEU cc_start: 0.9609 (OUTLIER) cc_final: 0.9337 (mp) REVERT: D 244 ASN cc_start: 0.8814 (m110) cc_final: 0.8475 (m-40) REVERT: D 270 GLU cc_start: 0.9121 (mt-10) cc_final: 0.8836 (pt0) REVERT: D 284 MET cc_start: 0.9563 (tmm) cc_final: 0.8937 (tmm) REVERT: A 4 PHE cc_start: 0.8487 (m-80) cc_final: 0.8005 (m-80) REVERT: A 21 ASP cc_start: 0.8964 (t0) cc_final: 0.8685 (t0) REVERT: A 75 CYS cc_start: 0.9631 (OUTLIER) cc_final: 0.9392 (p) REVERT: A 99 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.8275 (mmm) REVERT: A 104 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.8236 (mtp85) REVERT: A 117 ASP cc_start: 0.8927 (t0) cc_final: 0.8353 (t0) REVERT: A 168 LYS cc_start: 0.9230 (mmmt) cc_final: 0.8830 (mmmt) REVERT: A 171 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8698 (t) REVERT: A 172 LYS cc_start: 0.9239 (mppt) cc_final: 0.8940 (mmtm) REVERT: G 32 ARG cc_start: 0.8711 (ttp80) cc_final: 0.8259 (ttt-90) REVERT: G 137 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8778 (p) REVERT: H 8 THR cc_start: 0.9470 (OUTLIER) cc_final: 0.9197 (p) REVERT: H 117 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8646 (tm-30) REVERT: H 162 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8144 (ptp-110) REVERT: H 172 TYR cc_start: 0.9047 (t80) cc_final: 0.8528 (t80) REVERT: F 1027 GLN cc_start: 0.8889 (mt0) cc_final: 0.8517 (mt0) REVERT: F 1055 TYR cc_start: 0.7959 (p90) cc_final: 0.7522 (p90) REVERT: F 1163 VAL cc_start: 0.9337 (OUTLIER) cc_final: 0.9111 (t) outliers start: 55 outliers final: 33 residues processed: 227 average time/residue: 0.2427 time to fit residues: 80.8989 Evaluate side-chains 228 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 180 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 169 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1142 VAL Chi-restraints excluded: chain F residue 1163 VAL Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 153 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 106 optimal weight: 0.0570 chunk 161 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 128 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13479 Z= 0.180 Angle : 0.682 12.975 18235 Z= 0.328 Chirality : 0.045 0.374 2081 Planarity : 0.003 0.038 2327 Dihedral : 6.249 57.934 1832 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.44 % Favored : 95.38 % Rotamer: Outliers : 3.36 % Allowed : 26.64 % Favored : 70.00 % 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: 0.17 (0.21), residues: 1667 helix: 1.31 (0.19), residues: 736 sheet: -1.11 (0.29), residues: 321 loop : -0.54 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 263 HIS 0.009 0.001 HIS D 304 PHE 0.042 0.001 PHE C 264 TYR 0.032 0.002 TYR C 307 ARG 0.009 0.001 ARG D 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 189 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.8211 (ppp) cc_final: 0.7834 (ppp) REVERT: B 13 GLN cc_start: 0.9818 (OUTLIER) cc_final: 0.9225 (mp10) REVERT: B 106 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8846 (mm) REVERT: B 182 HIS cc_start: 0.8656 (m90) cc_final: 0.8273 (m-70) REVERT: B 284 MET cc_start: 0.9700 (tmm) cc_final: 0.9332 (tmm) REVERT: B 307 TYR cc_start: 0.8999 (t80) cc_final: 0.8583 (t80) REVERT: E 98 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8533 (p0) REVERT: E 112 SER cc_start: 0.8300 (m) cc_final: 0.7913 (p) REVERT: E 120 HIS cc_start: 0.8586 (m170) cc_final: 0.8297 (m170) REVERT: E 137 THR cc_start: 0.9142 (OUTLIER) cc_final: 0.8300 (p) REVERT: E 168 MET cc_start: 0.8799 (mtt) cc_final: 0.8400 (mtt) REVERT: E 285 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.7981 (t80) REVERT: E 297 ILE cc_start: 0.8804 (mm) cc_final: 0.8482 (tt) REVERT: C 302 GLU cc_start: 0.9109 (OUTLIER) cc_final: 0.8898 (pm20) REVERT: C 305 LEU cc_start: 0.9606 (OUTLIER) cc_final: 0.9360 (mp) REVERT: D 244 ASN cc_start: 0.8791 (m110) cc_final: 0.8440 (m-40) REVERT: D 270 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8821 (pt0) REVERT: D 284 MET cc_start: 0.9524 (tmm) cc_final: 0.8855 (tmm) REVERT: A 4 PHE cc_start: 0.8471 (m-80) cc_final: 0.7997 (m-80) REVERT: A 21 ASP cc_start: 0.8982 (t0) cc_final: 0.8654 (t0) REVERT: A 75 CYS cc_start: 0.9628 (OUTLIER) cc_final: 0.9376 (p) REVERT: A 99 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8075 (mmm) REVERT: A 104 ARG cc_start: 0.8629 (mtt-85) cc_final: 0.8315 (mmp80) REVERT: A 117 ASP cc_start: 0.8929 (t0) cc_final: 0.8344 (t0) REVERT: A 168 LYS cc_start: 0.9223 (mmmt) cc_final: 0.8827 (mmmt) REVERT: A 171 THR cc_start: 0.8938 (OUTLIER) cc_final: 0.8705 (t) REVERT: A 172 LYS cc_start: 0.9235 (mppt) cc_final: 0.8933 (mmtm) REVERT: G 32 ARG cc_start: 0.8659 (ttp80) cc_final: 0.8239 (ttt-90) REVERT: G 134 GLN cc_start: 0.8665 (mp10) cc_final: 0.8372 (pm20) REVERT: G 137 THR cc_start: 0.9092 (OUTLIER) cc_final: 0.8756 (p) REVERT: H 8 THR cc_start: 0.9460 (OUTLIER) cc_final: 0.9178 (p) REVERT: H 117 GLU cc_start: 0.8887 (OUTLIER) cc_final: 0.8661 (tm-30) REVERT: H 162 ARG cc_start: 0.8535 (ttm110) cc_final: 0.8117 (ptp-110) REVERT: H 172 TYR cc_start: 0.9028 (t80) cc_final: 0.8525 (t80) REVERT: F 1027 GLN cc_start: 0.8859 (mt0) cc_final: 0.8458 (mt0) REVERT: F 1055 TYR cc_start: 0.7854 (p90) cc_final: 0.7415 (p90) outliers start: 48 outliers final: 32 residues processed: 223 average time/residue: 0.2429 time to fit residues: 79.6927 Evaluate side-chains 231 residues out of total 1430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 186 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 89 THR Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 109 PHE Chi-restraints excluded: chain B residue 120 HIS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain E residue 3 THR Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 152 CYS Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 297 ILE Chi-restraints excluded: chain C residue 302 GLU Chi-restraints excluded: chain C residue 305 LEU Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 271 GLU Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 49 ASN Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 163 THR Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain G residue 2 LYS Chi-restraints excluded: chain G residue 13 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain G residue 147 ILE Chi-restraints excluded: chain H residue 8 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 117 GLU Chi-restraints excluded: chain H residue 163 VAL Chi-restraints excluded: chain F residue 1142 VAL Chi-restraints excluded: chain F residue 1197 LEU Chi-restraints excluded: chain F residue 1227 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 136 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 128 optimal weight: 0.2980 chunk 53 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 0.2980 chunk 113 optimal weight: 6.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 149 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 13 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.055249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.040079 restraints weight = 51076.828| |-----------------------------------------------------------------------------| r_work (start): 0.2657 rms_B_bonded: 4.45 r_work: 0.2499 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13479 Z= 0.209 Angle : 0.686 12.638 18235 Z= 0.329 Chirality : 0.045 0.355 2081 Planarity : 0.003 0.038 2327 Dihedral : 6.258 59.163 1832 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.38 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.50 % Favored : 95.32 % Rotamer: Outliers : 3.64 % Allowed : 26.43 % Favored : 69.93 % 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: 0.25 (0.21), residues: 1667 helix: 1.34 (0.19), residues: 732 sheet: -0.93 (0.30), residues: 301 loop : -0.56 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 263 HIS 0.009 0.001 HIS D 304 PHE 0.030 0.001 PHE C 264 TYR 0.040 0.002 TYR D 261 ARG 0.008 0.001 ARG F1131 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2831.26 seconds wall clock time: 51 minutes 30.06 seconds (3090.06 seconds total)