Starting phenix.real_space_refine on Wed Feb 14 06:06:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7db6_30627/02_2024/7db6_30627_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7db6_30627/02_2024/7db6_30627.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7db6_30627/02_2024/7db6_30627_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7db6_30627/02_2024/7db6_30627_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7db6_30627/02_2024/7db6_30627_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7db6_30627/02_2024/7db6_30627.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7db6_30627/02_2024/7db6_30627.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7db6_30627/02_2024/7db6_30627_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7db6_30627/02_2024/7db6_30627_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5600 2.51 5 N 1479 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 26": "OD1" <-> "OD2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A PHE 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 328": "OD1" <-> "OD2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C GLU 42": "OE1" <-> "OE2" Residue "E PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 171": "OD1" <-> "OD2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D TYR 282": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8767 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1764 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 2 Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "D" Number of atoms: 2229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2229 Unusual residues: {'JEV': 1} Classifications: {'peptide': 276, 'undetermined': 1} Link IDs: {'PTRANS': 11, 'TRANS': 264, None: 1} Not linked: pdbres="TYR D 306 " pdbres="JEV D 401 " Chain breaks: 1 Time building chain proxies: 5.19, per 1000 atoms: 0.59 Number of scatterers: 8767 At special positions: 0 Unit cell: (128.246, 125.364, 89.3401, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1626 8.00 N 1479 7.00 C 5600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 103 " - pdb=" SG CYS B 114 " distance=2.05 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS D 100 " - pdb=" SG CYS D 177 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 13 sheets defined 28.3% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 9 through 31 removed outlier: 4.268A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 228 through 230 No H-bonds generated for 'chain 'A' and resid 228 through 230' Processing helix chain 'A' and resid 243 through 253 Processing helix chain 'A' and resid 278 through 280 No H-bonds generated for 'chain 'A' and resid 278 through 280' Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 337 through 351 removed outlier: 4.248A pdb=" N VAL A 342 " --> pdb=" O ALA A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.991A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 21 Processing helix chain 'C' and resid 34 through 43 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'D' and resid 25 through 50 removed outlier: 4.658A pdb=" N ALA D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N CYS D 32 " --> pdb=" O SER D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 78 removed outlier: 4.027A pdb=" N VAL D 76 " --> pdb=" O ALA D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 90 Processing helix chain 'D' and resid 97 through 129 removed outlier: 3.786A pdb=" N GLY D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 138 No H-bonds generated for 'chain 'D' and resid 135 through 138' Processing helix chain 'D' and resid 143 through 160 Processing helix chain 'D' and resid 185 through 192 removed outlier: 3.757A pdb=" N VAL D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 216 Processing helix chain 'D' and resid 234 through 241 removed outlier: 4.808A pdb=" N MET D 240 " --> pdb=" O ASN D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 245 through 260 Proline residue: D 253 - end of helix Processing helix chain 'D' and resid 265 through 271 removed outlier: 3.525A pdb=" N VAL D 269 " --> pdb=" O PRO D 265 " (cutoff:3.500A) Proline residue: D 270 - end of helix No H-bonds generated for 'chain 'D' and resid 265 through 271' Processing helix chain 'D' and resid 274 through 297 removed outlier: 3.723A pdb=" N ALA D 284 " --> pdb=" O SER D 280 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 288 " --> pdb=" O ALA D 284 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS D 289 " --> pdb=" O TYR D 285 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA D 292 " --> pdb=" O SER D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 303 No H-bonds generated for 'chain 'D' and resid 300 through 303' Processing sheet with id= A, first strand: chain 'A' and resid 220 through 224 removed outlier: 3.855A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.105A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.165A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 165 through 168 Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.865A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.979A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.647A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.323A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.619A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ALA E 40 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LEU E 45 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'E' and resid 128 through 130 Processing sheet with id= M, first strand: chain 'E' and resid 231 through 233 removed outlier: 3.732A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 334 hydrogen bonds defined for protein. 960 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.55 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2797 1.34 - 1.47: 2236 1.47 - 1.59: 3834 1.59 - 1.71: 0 1.71 - 1.83: 88 Bond restraints: 8955 Sorted by residual: bond pdb=" C3 JEV D 401 " pdb=" N1 JEV D 401 " ideal model delta sigma weight residual 1.452 1.330 0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C ARG D 22 " pdb=" N PRO D 23 " ideal model delta sigma weight residual 1.334 1.380 -0.046 8.40e-03 1.42e+04 3.06e+01 bond pdb=" C12 JEV D 401 " pdb=" O1 JEV D 401 " ideal model delta sigma weight residual 1.488 1.379 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C6 JEV D 401 " pdb=" C7 JEV D 401 " ideal model delta sigma weight residual 1.495 1.552 -0.057 2.00e-02 2.50e+03 8.00e+00 bond pdb=" C8 JEV D 401 " pdb=" C9 JEV D 401 " ideal model delta sigma weight residual 1.553 1.503 0.050 2.00e-02 2.50e+03 6.28e+00 ... (remaining 8950 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.29: 130 105.29 - 112.48: 4424 112.48 - 119.67: 3185 119.67 - 126.86: 4278 126.86 - 134.05: 120 Bond angle restraints: 12137 Sorted by residual: angle pdb=" N ARG D 59 " pdb=" CA ARG D 59 " pdb=" CB ARG D 59 " ideal model delta sigma weight residual 114.17 108.97 5.20 1.14e+00 7.69e-01 2.08e+01 angle pdb=" CA LYS D 56 " pdb=" CB LYS D 56 " pdb=" CG LYS D 56 " ideal model delta sigma weight residual 114.10 122.33 -8.23 2.00e+00 2.50e-01 1.69e+01 angle pdb=" C GLN E 219 " pdb=" N HIS E 220 " pdb=" CA HIS E 220 " ideal model delta sigma weight residual 121.54 113.83 7.71 1.91e+00 2.74e-01 1.63e+01 angle pdb=" C LEU A 232 " pdb=" N VAL A 233 " pdb=" CA VAL A 233 " ideal model delta sigma weight residual 121.70 128.58 -6.88 1.80e+00 3.09e-01 1.46e+01 angle pdb=" N ILE D 174 " pdb=" CA ILE D 174 " pdb=" C ILE D 174 " ideal model delta sigma weight residual 109.34 101.40 7.94 2.08e+00 2.31e-01 1.46e+01 ... (remaining 12132 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4722 17.94 - 35.87: 503 35.87 - 53.81: 71 53.81 - 71.74: 6 71.74 - 89.68: 3 Dihedral angle restraints: 5305 sinusoidal: 2063 harmonic: 3242 Sorted by residual: dihedral pdb=" CA PHE B 292 " pdb=" C PHE B 292 " pdb=" N ASN B 293 " pdb=" CA ASN B 293 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY B 310 " pdb=" C GLY B 310 " pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta harmonic sigma weight residual 180.00 152.09 27.91 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CB CYS B 103 " pdb=" SG CYS B 103 " pdb=" SG CYS B 114 " pdb=" CB CYS B 114 " ideal model delta sinusoidal sigma weight residual -86.00 -131.67 45.67 1 1.00e+01 1.00e-02 2.89e+01 ... (remaining 5302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1034 0.059 - 0.118: 269 0.118 - 0.177: 62 0.177 - 0.236: 7 0.236 - 0.294: 2 Chirality restraints: 1374 Sorted by residual: chirality pdb=" CB VAL D 198 " pdb=" CA VAL D 198 " pdb=" CG1 VAL D 198 " pdb=" CG2 VAL D 198 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA TYR E 178 " pdb=" N TYR E 178 " pdb=" C TYR E 178 " pdb=" CB TYR E 178 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CB ILE B 157 " pdb=" CA ILE B 157 " pdb=" CG1 ILE B 157 " pdb=" CG2 ILE B 157 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.22 2.00e-01 2.50e+01 1.26e+00 ... (remaining 1371 not shown) Planarity restraints: 1530 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU D 58 " 0.015 2.00e-02 2.50e+03 3.09e-02 9.58e+00 pdb=" C LEU D 58 " -0.054 2.00e-02 2.50e+03 pdb=" O LEU D 58 " 0.020 2.00e-02 2.50e+03 pdb=" N ARG D 59 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL D 198 " -0.051 5.00e-02 4.00e+02 7.61e-02 9.28e+00 pdb=" N PRO D 199 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO D 199 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 199 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 JEV D 401 " 0.021 2.00e-02 2.50e+03 1.89e-02 8.96e+00 pdb=" C11 JEV D 401 " 0.019 2.00e-02 2.50e+03 pdb=" C12 JEV D 401 " 0.002 2.00e-02 2.50e+03 pdb=" C13 JEV D 401 " -0.002 2.00e-02 2.50e+03 pdb=" C14 JEV D 401 " 0.019 2.00e-02 2.50e+03 pdb=" C16 JEV D 401 " -0.003 2.00e-02 2.50e+03 pdb=" C6 JEV D 401 " 0.010 2.00e-02 2.50e+03 pdb=" C8 JEV D 401 " -0.030 2.00e-02 2.50e+03 pdb=" C9 JEV D 401 " 0.002 2.00e-02 2.50e+03 pdb=" O1 JEV D 401 " -0.037 2.00e-02 2.50e+03 ... (remaining 1527 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1541 2.77 - 3.30: 7858 3.30 - 3.83: 14675 3.83 - 4.37: 17092 4.37 - 4.90: 29623 Nonbonded interactions: 70789 Sorted by model distance: nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.233 2.440 nonbonded pdb=" OH TYR A 320 " pdb=" OD2 ASP A 341 " model vdw 2.275 2.440 nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR E 163 " model vdw 2.285 2.440 nonbonded pdb=" O ASN A 256 " pdb=" OG1 THR A 260 " model vdw 2.297 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.298 2.440 ... (remaining 70784 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.190 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 27.770 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.122 8955 Z= 0.391 Angle : 0.975 12.803 12137 Z= 0.535 Chirality : 0.057 0.294 1374 Planarity : 0.007 0.076 1530 Dihedral : 14.193 89.679 3205 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.01 % Favored : 92.90 % Rotamer: Outliers : 0.63 % Allowed : 8.67 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -4.08 (0.21), residues: 1098 helix: -2.93 (0.20), residues: 345 sheet: -2.22 (0.27), residues: 264 loop : -2.69 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.006 0.002 HIS E 35 PHE 0.024 0.003 PHE A 189 TYR 0.029 0.002 TYR E 178 ARG 0.005 0.001 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6553 (ttm) cc_final: 0.6179 (ttt) REVERT: A 29 LYS cc_start: 0.7616 (mppt) cc_final: 0.7035 (mmmt) REVERT: A 197 LYS cc_start: 0.8072 (mtpt) cc_final: 0.7201 (mttm) REVERT: B 61 MET cc_start: 0.8709 (tmm) cc_final: 0.8360 (ppp) REVERT: B 217 MET cc_start: 0.6460 (ttp) cc_final: 0.5701 (tmm) REVERT: B 239 ASN cc_start: 0.7775 (m-40) cc_final: 0.7492 (t0) REVERT: B 271 CYS cc_start: 0.6295 (p) cc_final: 0.5984 (m) REVERT: B 280 LYS cc_start: 0.8129 (tttt) cc_final: 0.7836 (tptt) REVERT: E 64 VAL cc_start: 0.8215 (m) cc_final: 0.7812 (t) REVERT: E 87 ARG cc_start: 0.7091 (mpt90) cc_final: 0.6683 (mtp180) REVERT: E 93 MET cc_start: 0.7257 (tpp) cc_final: 0.6814 (tpp) REVERT: E 208 GLU cc_start: 0.7733 (tt0) cc_final: 0.7468 (mm-30) REVERT: E 222 GLU cc_start: 0.7706 (tt0) cc_final: 0.7425 (tt0) REVERT: E 232 LYS cc_start: 0.7917 (ttpt) cc_final: 0.7643 (ttpp) REVERT: D 34 LEU cc_start: 0.7090 (tt) cc_final: 0.6633 (mt) REVERT: D 107 MET cc_start: 0.5796 (ttm) cc_final: 0.4935 (tmm) REVERT: D 116 PHE cc_start: 0.7878 (m-10) cc_final: 0.7632 (m-10) REVERT: D 126 TYR cc_start: 0.8098 (t80) cc_final: 0.7631 (t80) REVERT: D 131 HIS cc_start: 0.6741 (t70) cc_final: 0.6347 (t-170) REVERT: D 154 LEU cc_start: 0.6121 (tt) cc_final: 0.5920 (mt) REVERT: D 179 PHE cc_start: 0.6708 (t80) cc_final: 0.6352 (t80) REVERT: D 277 PHE cc_start: 0.5699 (t80) cc_final: 0.5478 (t80) REVERT: D 293 ILE cc_start: 0.7354 (mm) cc_final: 0.6975 (mm) outliers start: 6 outliers final: 0 residues processed: 193 average time/residue: 0.2178 time to fit residues: 57.0970 Evaluate side-chains 137 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 45 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 88 ASN B 91 HIS B 142 HIS B 176 GLN B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 117 ASN D 143 ASN D 255 ASN ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6765 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 8955 Z= 0.205 Angle : 0.649 17.537 12137 Z= 0.338 Chirality : 0.043 0.211 1374 Planarity : 0.005 0.052 1530 Dihedral : 6.657 74.980 1223 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.01 % Favored : 93.90 % Rotamer: Outliers : 2.82 % Allowed : 13.90 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -3.25 (0.22), residues: 1098 helix: -1.70 (0.25), residues: 350 sheet: -1.93 (0.29), residues: 249 loop : -2.54 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.017 0.002 PHE A 189 TYR 0.027 0.001 TYR E 178 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 162 time to evaluate : 1.051 Fit side-chains revert: symmetry clash REVERT: A 18 MET cc_start: 0.6437 (ttm) cc_final: 0.6107 (ttt) REVERT: A 29 LYS cc_start: 0.7488 (mppt) cc_final: 0.7009 (mmmt) REVERT: A 33 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7310 (mt-10) REVERT: A 185 VAL cc_start: 0.7683 (OUTLIER) cc_final: 0.7342 (m) REVERT: A 197 LYS cc_start: 0.8075 (mtpt) cc_final: 0.6936 (mttm) REVERT: A 247 MET cc_start: 0.3519 (mmt) cc_final: 0.3244 (mmp) REVERT: A 349 LYS cc_start: 0.8189 (tttt) cc_final: 0.7558 (ttmm) REVERT: B 61 MET cc_start: 0.8649 (tmm) cc_final: 0.8295 (ppp) REVERT: B 239 ASN cc_start: 0.7686 (m-40) cc_final: 0.7461 (t0) REVERT: B 247 ASP cc_start: 0.6468 (t0) cc_final: 0.6088 (t0) REVERT: B 262 MET cc_start: 0.7624 (mtm) cc_final: 0.7224 (mtp) REVERT: B 271 CYS cc_start: 0.6421 (p) cc_final: 0.5864 (m) REVERT: B 280 LYS cc_start: 0.8204 (tttt) cc_final: 0.7633 (tptt) REVERT: C 32 LYS cc_start: 0.6982 (mptt) cc_final: 0.6469 (ptpt) REVERT: E 34 MET cc_start: 0.7813 (mmp) cc_final: 0.7420 (mmp) REVERT: E 64 VAL cc_start: 0.8251 (m) cc_final: 0.7809 (t) REVERT: E 74 ASP cc_start: 0.7593 (m-30) cc_final: 0.7306 (m-30) REVERT: E 87 ARG cc_start: 0.7232 (mpt90) cc_final: 0.6758 (mtp180) REVERT: E 93 MET cc_start: 0.7385 (tpp) cc_final: 0.6741 (tpp) REVERT: E 208 GLU cc_start: 0.7859 (tt0) cc_final: 0.7477 (mm-30) REVERT: E 210 GLU cc_start: 0.7095 (pp20) cc_final: 0.6643 (pp20) REVERT: E 222 GLU cc_start: 0.7694 (tt0) cc_final: 0.7374 (tt0) REVERT: E 232 LYS cc_start: 0.8222 (ttpt) cc_final: 0.7931 (ttmt) REVERT: D 107 MET cc_start: 0.5561 (ttm) cc_final: 0.4996 (ttm) REVERT: D 131 HIS cc_start: 0.6937 (t70) cc_final: 0.6615 (t70) REVERT: D 237 PHE cc_start: 0.7180 (t80) cc_final: 0.6970 (t80) REVERT: D 251 TRP cc_start: 0.7372 (m100) cc_final: 0.6654 (m100) REVERT: D 293 ILE cc_start: 0.7330 (mm) cc_final: 0.6937 (mm) REVERT: D 300 GLN cc_start: 0.8024 (pm20) cc_final: 0.6893 (pm20) REVERT: D 305 GLU cc_start: 0.4900 (tm-30) cc_final: 0.4657 (tt0) outliers start: 27 outliers final: 17 residues processed: 180 average time/residue: 0.2141 time to fit residues: 52.5924 Evaluate side-chains 161 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 10.0000 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 8955 Z= 0.299 Angle : 0.671 11.986 12137 Z= 0.355 Chirality : 0.045 0.237 1374 Planarity : 0.005 0.055 1530 Dihedral : 6.693 87.526 1223 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.56 % Favored : 92.35 % Rotamer: Outliers : 4.08 % Allowed : 17.35 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.78 (0.24), residues: 1098 helix: -1.08 (0.26), residues: 348 sheet: -1.97 (0.27), residues: 286 loop : -2.23 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 82 HIS 0.005 0.001 HIS E 35 PHE 0.026 0.002 PHE B 253 TYR 0.028 0.002 TYR E 178 ARG 0.008 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 156 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6578 (ttm) cc_final: 0.6170 (ttt) REVERT: A 185 VAL cc_start: 0.7612 (OUTLIER) cc_final: 0.7207 (m) REVERT: A 197 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7188 (mttm) REVERT: A 349 LYS cc_start: 0.8102 (tttt) cc_final: 0.7518 (ttmm) REVERT: B 61 MET cc_start: 0.8573 (tmm) cc_final: 0.8044 (ppp) REVERT: B 239 ASN cc_start: 0.7766 (m-40) cc_final: 0.7366 (t0) REVERT: B 247 ASP cc_start: 0.6975 (t0) cc_final: 0.6622 (t0) REVERT: B 262 MET cc_start: 0.7779 (mtm) cc_final: 0.7329 (mtp) REVERT: B 271 CYS cc_start: 0.6547 (p) cc_final: 0.5888 (m) REVERT: B 280 LYS cc_start: 0.8289 (tttt) cc_final: 0.7831 (tptt) REVERT: E 19 LYS cc_start: 0.8302 (tttt) cc_final: 0.8040 (tttm) REVERT: E 46 GLU cc_start: 0.6794 (tt0) cc_final: 0.6404 (tt0) REVERT: E 62 ASP cc_start: 0.8245 (m-30) cc_final: 0.7871 (m-30) REVERT: E 87 ARG cc_start: 0.7322 (mpt90) cc_final: 0.6938 (mtp180) REVERT: E 93 MET cc_start: 0.7351 (tpp) cc_final: 0.6440 (tpp) REVERT: E 208 GLU cc_start: 0.8045 (tt0) cc_final: 0.7443 (mm-30) REVERT: E 210 GLU cc_start: 0.6901 (pp20) cc_final: 0.6427 (pp20) REVERT: E 219 GLN cc_start: 0.8159 (pp30) cc_final: 0.7927 (pp30) REVERT: E 222 GLU cc_start: 0.7751 (tt0) cc_final: 0.7476 (tt0) REVERT: E 232 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7799 (ttmm) REVERT: D 107 MET cc_start: 0.5633 (ttm) cc_final: 0.5065 (ttm) REVERT: D 131 HIS cc_start: 0.7106 (t70) cc_final: 0.6744 (t70) REVERT: D 245 VAL cc_start: 0.6463 (OUTLIER) cc_final: 0.6224 (p) REVERT: D 293 ILE cc_start: 0.7539 (mm) cc_final: 0.7174 (mm) REVERT: D 300 GLN cc_start: 0.7713 (pm20) cc_final: 0.6980 (pm20) outliers start: 39 outliers final: 27 residues processed: 183 average time/residue: 0.2251 time to fit residues: 56.1811 Evaluate side-chains 179 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 150 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 9.9990 chunk 74 optimal weight: 0.0040 chunk 51 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 105 optimal weight: 30.0000 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 8955 Z= 0.315 Angle : 0.673 11.947 12137 Z= 0.355 Chirality : 0.045 0.229 1374 Planarity : 0.005 0.052 1530 Dihedral : 6.594 86.977 1223 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.29 % Favored : 92.62 % Rotamer: Outliers : 4.28 % Allowed : 19.02 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.55 (0.24), residues: 1098 helix: -0.74 (0.27), residues: 343 sheet: -1.87 (0.28), residues: 286 loop : -2.19 (0.27), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS E 35 PHE 0.025 0.002 PHE B 253 TYR 0.028 0.002 TYR E 178 ARG 0.006 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 155 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6618 (ttm) cc_final: 0.6290 (ttt) REVERT: A 185 VAL cc_start: 0.7527 (OUTLIER) cc_final: 0.7192 (m) REVERT: A 197 LYS cc_start: 0.8092 (mtpt) cc_final: 0.7171 (mttm) REVERT: A 266 LEU cc_start: 0.4343 (OUTLIER) cc_final: 0.3601 (mm) REVERT: A 349 LYS cc_start: 0.8107 (tttt) cc_final: 0.7566 (ttmm) REVERT: B 61 MET cc_start: 0.8552 (tmm) cc_final: 0.8053 (ppp) REVERT: B 210 LEU cc_start: 0.8494 (tp) cc_final: 0.8287 (tp) REVERT: B 239 ASN cc_start: 0.7777 (m-40) cc_final: 0.7365 (t0) REVERT: B 247 ASP cc_start: 0.7057 (t0) cc_final: 0.6710 (t0) REVERT: B 262 MET cc_start: 0.7855 (mtm) cc_final: 0.7350 (mtp) REVERT: B 271 CYS cc_start: 0.6350 (p) cc_final: 0.5201 (m) REVERT: B 280 LYS cc_start: 0.8275 (tttt) cc_final: 0.7828 (tptt) REVERT: C 46 LYS cc_start: 0.6892 (mmmt) cc_final: 0.6658 (mmmt) REVERT: E 19 LYS cc_start: 0.8312 (tttt) cc_final: 0.8065 (tttm) REVERT: E 46 GLU cc_start: 0.7021 (tt0) cc_final: 0.6784 (tm-30) REVERT: E 62 ASP cc_start: 0.8312 (m-30) cc_final: 0.7976 (m-30) REVERT: E 87 ARG cc_start: 0.7263 (mpt90) cc_final: 0.6971 (mtp180) REVERT: E 93 MET cc_start: 0.7257 (tpp) cc_final: 0.6419 (tpp) REVERT: E 208 GLU cc_start: 0.7792 (tt0) cc_final: 0.6868 (mm-30) REVERT: E 210 GLU cc_start: 0.6770 (pp20) cc_final: 0.6410 (pp20) REVERT: E 220 HIS cc_start: 0.6691 (OUTLIER) cc_final: 0.6424 (t-90) REVERT: E 232 LYS cc_start: 0.8205 (ttpt) cc_final: 0.7909 (ttmm) REVERT: E 234 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7652 (mm-30) REVERT: D 86 MET cc_start: 0.7351 (ttt) cc_final: 0.7029 (tmm) REVERT: D 107 MET cc_start: 0.5609 (ttm) cc_final: 0.5028 (ttm) REVERT: D 131 HIS cc_start: 0.7031 (t70) cc_final: 0.6693 (t70) REVERT: D 169 GLN cc_start: 0.8351 (pp30) cc_final: 0.7586 (pp30) REVERT: D 241 PHE cc_start: 0.5424 (OUTLIER) cc_final: 0.5146 (m-80) REVERT: D 245 VAL cc_start: 0.6151 (OUTLIER) cc_final: 0.5923 (p) REVERT: D 251 TRP cc_start: 0.6741 (m100) cc_final: 0.6348 (m100) REVERT: D 293 ILE cc_start: 0.7569 (mm) cc_final: 0.7140 (mm) REVERT: D 300 GLN cc_start: 0.7715 (pm20) cc_final: 0.7016 (pm20) outliers start: 41 outliers final: 31 residues processed: 181 average time/residue: 0.2137 time to fit residues: 53.1026 Evaluate side-chains 184 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 148 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 241 PHE Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 288 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 GLN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8955 Z= 0.255 Angle : 0.633 12.717 12137 Z= 0.332 Chirality : 0.043 0.217 1374 Planarity : 0.004 0.048 1530 Dihedral : 6.290 85.634 1223 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.92 % Favored : 92.99 % Rotamer: Outliers : 4.81 % Allowed : 19.96 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.29 (0.24), residues: 1098 helix: -0.50 (0.28), residues: 347 sheet: -1.73 (0.29), residues: 284 loop : -2.06 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS B 225 PHE 0.022 0.002 PHE B 253 TYR 0.027 0.001 TYR E 178 ARG 0.007 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 152 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6605 (ttm) cc_final: 0.6212 (ttt) REVERT: A 185 VAL cc_start: 0.7470 (OUTLIER) cc_final: 0.7101 (m) REVERT: A 197 LYS cc_start: 0.8079 (mtpt) cc_final: 0.7089 (mttm) REVERT: A 266 LEU cc_start: 0.4388 (OUTLIER) cc_final: 0.3612 (mm) REVERT: A 349 LYS cc_start: 0.8072 (tttt) cc_final: 0.7552 (ttmm) REVERT: B 61 MET cc_start: 0.8544 (tmm) cc_final: 0.8071 (ppp) REVERT: B 124 TYR cc_start: 0.8598 (m-80) cc_final: 0.8273 (m-80) REVERT: B 234 PHE cc_start: 0.8572 (OUTLIER) cc_final: 0.7973 (m-80) REVERT: B 239 ASN cc_start: 0.7724 (m-40) cc_final: 0.7333 (t0) REVERT: B 247 ASP cc_start: 0.6811 (t0) cc_final: 0.6478 (t0) REVERT: B 262 MET cc_start: 0.7810 (mtm) cc_final: 0.7271 (mtp) REVERT: B 271 CYS cc_start: 0.6451 (p) cc_final: 0.5079 (m) REVERT: B 280 LYS cc_start: 0.8510 (tttt) cc_final: 0.7879 (tptt) REVERT: E 19 LYS cc_start: 0.8297 (tttt) cc_final: 0.7912 (ttmm) REVERT: E 46 GLU cc_start: 0.6793 (tt0) cc_final: 0.6425 (tt0) REVERT: E 62 ASP cc_start: 0.8328 (m-30) cc_final: 0.7975 (m-30) REVERT: E 87 ARG cc_start: 0.7308 (mpt90) cc_final: 0.7008 (mtp180) REVERT: E 93 MET cc_start: 0.7231 (tpp) cc_final: 0.6385 (tpp) REVERT: E 148 ARG cc_start: 0.7868 (mtm110) cc_final: 0.7657 (mtm110) REVERT: E 208 GLU cc_start: 0.7810 (tt0) cc_final: 0.6823 (mm-30) REVERT: E 210 GLU cc_start: 0.6741 (pp20) cc_final: 0.6403 (pp20) REVERT: E 232 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7894 (ttmm) REVERT: D 86 MET cc_start: 0.7425 (ttt) cc_final: 0.7209 (tmm) REVERT: D 107 MET cc_start: 0.5548 (ttm) cc_final: 0.5027 (ttm) REVERT: D 131 HIS cc_start: 0.6945 (t70) cc_final: 0.6588 (t70) REVERT: D 169 GLN cc_start: 0.8373 (pp30) cc_final: 0.7597 (pp30) REVERT: D 293 ILE cc_start: 0.7467 (mm) cc_final: 0.7048 (mm) REVERT: D 300 GLN cc_start: 0.7719 (pm20) cc_final: 0.7234 (pm20) outliers start: 46 outliers final: 34 residues processed: 188 average time/residue: 0.2084 time to fit residues: 53.7879 Evaluate side-chains 183 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 146 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 185 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 239 THR Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 105 optimal weight: 0.5980 chunk 87 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 55 optimal weight: 9.9990 chunk 101 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 8955 Z= 0.200 Angle : 0.601 11.710 12137 Z= 0.315 Chirality : 0.042 0.205 1374 Planarity : 0.004 0.044 1530 Dihedral : 5.987 82.687 1223 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.01 % Favored : 93.90 % Rotamer: Outliers : 3.97 % Allowed : 21.11 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.25), residues: 1098 helix: -0.27 (0.28), residues: 352 sheet: -1.49 (0.30), residues: 276 loop : -1.88 (0.28), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.019 0.001 PHE B 253 TYR 0.026 0.001 TYR E 178 ARG 0.007 0.000 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 150 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6559 (ttm) cc_final: 0.6167 (ttt) REVERT: A 197 LYS cc_start: 0.8103 (mtpt) cc_final: 0.7087 (mttm) REVERT: A 349 LYS cc_start: 0.8217 (tttt) cc_final: 0.7776 (ttmm) REVERT: B 61 MET cc_start: 0.8553 (tmm) cc_final: 0.8139 (ppp) REVERT: B 95 LEU cc_start: 0.6768 (OUTLIER) cc_final: 0.6450 (mt) REVERT: B 124 TYR cc_start: 0.8574 (m-80) cc_final: 0.8218 (m-80) REVERT: B 234 PHE cc_start: 0.8587 (OUTLIER) cc_final: 0.8020 (m-80) REVERT: B 239 ASN cc_start: 0.7722 (m-40) cc_final: 0.7309 (t0) REVERT: B 247 ASP cc_start: 0.6697 (t0) cc_final: 0.6356 (t0) REVERT: B 262 MET cc_start: 0.7721 (mtm) cc_final: 0.7146 (mtp) REVERT: B 271 CYS cc_start: 0.6350 (p) cc_final: 0.5125 (m) REVERT: B 280 LYS cc_start: 0.8406 (tttt) cc_final: 0.7786 (tptt) REVERT: E 74 ASP cc_start: 0.7599 (m-30) cc_final: 0.7147 (m-30) REVERT: E 87 ARG cc_start: 0.7400 (mpt90) cc_final: 0.7012 (mtp180) REVERT: E 93 MET cc_start: 0.7227 (tpp) cc_final: 0.6382 (tpp) REVERT: E 208 GLU cc_start: 0.7952 (tt0) cc_final: 0.7004 (mm-30) REVERT: E 232 LYS cc_start: 0.8212 (ttpt) cc_final: 0.7858 (ttmm) REVERT: D 131 HIS cc_start: 0.6922 (t70) cc_final: 0.6552 (t70) REVERT: D 169 GLN cc_start: 0.8369 (pp30) cc_final: 0.7567 (pp30) REVERT: D 293 ILE cc_start: 0.7381 (mm) cc_final: 0.6988 (mm) REVERT: D 300 GLN cc_start: 0.7655 (pm20) cc_final: 0.7192 (pm20) outliers start: 38 outliers final: 31 residues processed: 179 average time/residue: 0.2094 time to fit residues: 51.7296 Evaluate side-chains 174 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 234 PHE Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 288 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 10.0000 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 0.0570 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 58 optimal weight: 4.9990 chunk 105 optimal weight: 9.9990 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 8955 Z= 0.335 Angle : 0.684 11.346 12137 Z= 0.360 Chirality : 0.045 0.236 1374 Planarity : 0.005 0.046 1530 Dihedral : 6.336 84.235 1223 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.74 % Favored : 92.17 % Rotamer: Outliers : 4.81 % Allowed : 20.90 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % 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: -2.10 (0.25), residues: 1098 helix: -0.35 (0.27), residues: 354 sheet: -1.70 (0.29), residues: 287 loop : -1.90 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 275 HIS 0.005 0.002 HIS E 35 PHE 0.022 0.002 PHE B 253 TYR 0.029 0.002 TYR E 178 ARG 0.007 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 144 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6723 (ttm) cc_final: 0.6393 (ttt) REVERT: A 197 LYS cc_start: 0.7999 (mtpt) cc_final: 0.6604 (mmtp) REVERT: A 266 LEU cc_start: 0.4524 (OUTLIER) cc_final: 0.3725 (mm) REVERT: A 349 LYS cc_start: 0.7910 (tttt) cc_final: 0.7409 (ttmm) REVERT: B 61 MET cc_start: 0.8540 (tmm) cc_final: 0.8028 (ppp) REVERT: B 95 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6614 (mt) REVERT: B 124 TYR cc_start: 0.8672 (m-80) cc_final: 0.8202 (m-80) REVERT: B 142 HIS cc_start: 0.8266 (OUTLIER) cc_final: 0.5687 (m90) REVERT: B 163 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7719 (m-30) REVERT: B 234 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8098 (m-80) REVERT: B 247 ASP cc_start: 0.6874 (t0) cc_final: 0.6332 (t0) REVERT: B 262 MET cc_start: 0.7827 (mtm) cc_final: 0.7168 (mtp) REVERT: B 280 LYS cc_start: 0.8486 (tttt) cc_final: 0.7931 (tptt) REVERT: E 19 LYS cc_start: 0.8380 (tttt) cc_final: 0.8095 (tttm) REVERT: E 46 GLU cc_start: 0.6864 (tt0) cc_final: 0.6528 (tt0) REVERT: E 83 MET cc_start: 0.8514 (mtm) cc_final: 0.8091 (mtp) REVERT: E 87 ARG cc_start: 0.7245 (mpt90) cc_final: 0.7026 (mtp180) REVERT: E 93 MET cc_start: 0.7215 (tpp) cc_final: 0.6394 (tpp) REVERT: E 208 GLU cc_start: 0.7990 (tt0) cc_final: 0.7013 (mm-30) REVERT: E 232 LYS cc_start: 0.8309 (ttpt) cc_final: 0.7879 (ttmm) REVERT: D 131 HIS cc_start: 0.7001 (t70) cc_final: 0.6618 (t70) REVERT: D 169 GLN cc_start: 0.8376 (pp30) cc_final: 0.7597 (pp30) REVERT: D 255 ASN cc_start: 0.7638 (m-40) cc_final: 0.7409 (m110) REVERT: D 293 ILE cc_start: 0.7434 (mm) cc_final: 0.7037 (mm) REVERT: D 300 GLN cc_start: 0.7683 (pm20) cc_final: 0.7228 (pm20) outliers start: 46 outliers final: 35 residues processed: 182 average time/residue: 0.2174 time to fit residues: 53.9702 Evaluate side-chains 181 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 141 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 163 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 271 ARG Chi-restraints excluded: chain D residue 288 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.0040 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 71 optimal weight: 0.0040 chunk 51 optimal weight: 7.9990 chunk 9 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 overall best weight: 0.5204 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 8955 Z= 0.156 Angle : 0.622 13.385 12137 Z= 0.322 Chirality : 0.043 0.235 1374 Planarity : 0.004 0.043 1530 Dihedral : 5.765 78.517 1223 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.56 % Favored : 94.35 % Rotamer: Outliers : 3.87 % Allowed : 22.15 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.25), residues: 1098 helix: 0.05 (0.29), residues: 350 sheet: -1.36 (0.30), residues: 274 loop : -1.71 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.016 0.001 PHE B 253 TYR 0.025 0.001 TYR E 178 ARG 0.013 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 149 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6724 (ttm) cc_final: 0.6411 (ttt) REVERT: A 197 LYS cc_start: 0.8058 (mtpt) cc_final: 0.7030 (mttm) REVERT: A 349 LYS cc_start: 0.7572 (tttt) cc_final: 0.7126 (ttmm) REVERT: B 61 MET cc_start: 0.8441 (tmm) cc_final: 0.8167 (ppp) REVERT: B 95 LEU cc_start: 0.6797 (OUTLIER) cc_final: 0.6484 (mt) REVERT: B 101 MET cc_start: 0.8327 (mtp) cc_final: 0.8076 (mtp) REVERT: B 124 TYR cc_start: 0.8428 (m-80) cc_final: 0.8140 (m-80) REVERT: B 234 PHE cc_start: 0.8615 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: B 247 ASP cc_start: 0.6427 (t0) cc_final: 0.6199 (t0) REVERT: B 262 MET cc_start: 0.7739 (mtm) cc_final: 0.7144 (mtp) REVERT: B 280 LYS cc_start: 0.8403 (tttt) cc_final: 0.7744 (tptt) REVERT: E 74 ASP cc_start: 0.7529 (m-30) cc_final: 0.7103 (m-30) REVERT: E 83 MET cc_start: 0.8560 (mtm) cc_final: 0.8128 (mtp) REVERT: E 87 ARG cc_start: 0.7464 (mpt90) cc_final: 0.7073 (mtp180) REVERT: E 93 MET cc_start: 0.7167 (tpp) cc_final: 0.6332 (tpp) REVERT: E 208 GLU cc_start: 0.7803 (tt0) cc_final: 0.7028 (mm-30) REVERT: E 232 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7835 (ttmm) REVERT: D 86 MET cc_start: 0.7459 (tmm) cc_final: 0.7203 (tmm) REVERT: D 93 TRP cc_start: 0.2062 (OUTLIER) cc_final: 0.0136 (t60) REVERT: D 116 PHE cc_start: 0.7652 (m-10) cc_final: 0.7330 (m-10) REVERT: D 131 HIS cc_start: 0.6952 (t70) cc_final: 0.6539 (t70) REVERT: D 168 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6307 (tt) REVERT: D 169 GLN cc_start: 0.8328 (pp30) cc_final: 0.8028 (pp30) REVERT: D 300 GLN cc_start: 0.7668 (pm20) cc_final: 0.7346 (pm20) outliers start: 37 outliers final: 28 residues processed: 177 average time/residue: 0.2260 time to fit residues: 54.3306 Evaluate side-chains 176 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 144 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 93 TRP Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 271 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 7.9990 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 ASN ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 143 ASN D 255 ASN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8955 Z= 0.191 Angle : 0.637 12.765 12137 Z= 0.331 Chirality : 0.044 0.267 1374 Planarity : 0.004 0.057 1530 Dihedral : 5.764 79.316 1223 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.28 % Favored : 93.62 % Rotamer: Outliers : 3.76 % Allowed : 21.94 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.26), residues: 1098 helix: 0.14 (0.28), residues: 350 sheet: -1.26 (0.31), residues: 274 loop : -1.65 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.019 0.001 PHE B 253 TYR 0.026 0.001 TYR E 178 ARG 0.013 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 149 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6576 (ttm) cc_final: 0.6230 (ttt) REVERT: A 197 LYS cc_start: 0.7945 (mtpt) cc_final: 0.6552 (mmtp) REVERT: A 349 LYS cc_start: 0.7521 (tttt) cc_final: 0.7117 (ttmm) REVERT: A 350 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7012 (m-30) REVERT: B 61 MET cc_start: 0.8528 (tmm) cc_final: 0.8176 (ppp) REVERT: B 95 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6611 (mt) REVERT: B 101 MET cc_start: 0.8303 (mtp) cc_final: 0.8085 (mtp) REVERT: B 124 TYR cc_start: 0.8629 (m-80) cc_final: 0.8274 (m-80) REVERT: B 234 PHE cc_start: 0.8638 (OUTLIER) cc_final: 0.8174 (m-80) REVERT: B 262 MET cc_start: 0.7795 (mtm) cc_final: 0.7194 (mtp) REVERT: B 280 LYS cc_start: 0.8396 (tttt) cc_final: 0.7896 (tptt) REVERT: E 71 SER cc_start: 0.7549 (OUTLIER) cc_final: 0.7230 (p) REVERT: E 74 ASP cc_start: 0.7550 (m-30) cc_final: 0.7113 (m-30) REVERT: E 83 MET cc_start: 0.8581 (mtm) cc_final: 0.8142 (mtp) REVERT: E 87 ARG cc_start: 0.7393 (mpt90) cc_final: 0.7039 (mtp180) REVERT: E 93 MET cc_start: 0.7239 (tpp) cc_final: 0.6429 (tpp) REVERT: E 208 GLU cc_start: 0.7982 (tt0) cc_final: 0.7049 (mm-30) REVERT: E 232 LYS cc_start: 0.8218 (ttpt) cc_final: 0.7833 (ttmm) REVERT: D 93 TRP cc_start: 0.2314 (OUTLIER) cc_final: 0.0415 (t60) REVERT: D 116 PHE cc_start: 0.7747 (m-10) cc_final: 0.7460 (m-10) REVERT: D 131 HIS cc_start: 0.6866 (t70) cc_final: 0.6440 (t70) REVERT: D 168 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6198 (tt) REVERT: D 169 GLN cc_start: 0.8446 (pp30) cc_final: 0.7645 (pp30) REVERT: D 300 GLN cc_start: 0.7639 (pm20) cc_final: 0.7315 (pm20) outliers start: 36 outliers final: 28 residues processed: 178 average time/residue: 0.2193 time to fit residues: 53.0761 Evaluate side-chains 178 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 144 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 267 PHE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 93 TRP Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 271 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 0.0570 chunk 108 optimal weight: 4.9990 chunk 99 optimal weight: 0.0010 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 0.0970 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 0.0670 overall best weight: 0.1840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 220 HIS D 101 GLN ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8955 Z= 0.148 Angle : 0.603 10.816 12137 Z= 0.312 Chirality : 0.042 0.208 1374 Planarity : 0.004 0.059 1530 Dihedral : 5.379 76.319 1223 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.37 % Favored : 94.54 % Rotamer: Outliers : 3.66 % Allowed : 22.88 % Favored : 73.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.26), residues: 1098 helix: 0.28 (0.29), residues: 352 sheet: -1.07 (0.31), residues: 269 loop : -1.62 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP B 82 HIS 0.004 0.001 HIS B 311 PHE 0.012 0.001 PHE E 200 TYR 0.020 0.001 TYR E 178 ARG 0.015 0.001 ARG E 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 148 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 MET cc_start: 0.6636 (ttm) cc_final: 0.6305 (ttt) REVERT: A 197 LYS cc_start: 0.7938 (mtpt) cc_final: 0.6544 (mmtp) REVERT: A 257 LYS cc_start: 0.4987 (OUTLIER) cc_final: 0.4453 (mptt) REVERT: A 349 LYS cc_start: 0.7475 (tttt) cc_final: 0.7136 (ttmm) REVERT: A 350 ASP cc_start: 0.7240 (OUTLIER) cc_final: 0.6878 (m-30) REVERT: B 61 MET cc_start: 0.8379 (tmm) cc_final: 0.7814 (ppp) REVERT: B 118 ASP cc_start: 0.7577 (p0) cc_final: 0.7175 (t0) REVERT: B 234 PHE cc_start: 0.8642 (OUTLIER) cc_final: 0.8229 (m-80) REVERT: B 262 MET cc_start: 0.7696 (mtm) cc_final: 0.7110 (mtp) REVERT: B 271 CYS cc_start: 0.6721 (p) cc_final: 0.5814 (m) REVERT: B 280 LYS cc_start: 0.8274 (tttt) cc_final: 0.7843 (tptt) REVERT: E 74 ASP cc_start: 0.7741 (m-30) cc_final: 0.7344 (m-30) REVERT: E 83 MET cc_start: 0.8377 (mtm) cc_final: 0.7941 (mtp) REVERT: E 87 ARG cc_start: 0.7539 (mpt90) cc_final: 0.7332 (mtp180) REVERT: E 93 MET cc_start: 0.7336 (tpp) cc_final: 0.6538 (tpp) REVERT: E 208 GLU cc_start: 0.8040 (tt0) cc_final: 0.7431 (mm-30) REVERT: D 93 TRP cc_start: 0.2055 (OUTLIER) cc_final: 0.0279 (t60) REVERT: D 116 PHE cc_start: 0.7630 (m-10) cc_final: 0.7353 (m-10) REVERT: D 131 HIS cc_start: 0.6861 (t70) cc_final: 0.6424 (t70) REVERT: D 147 TYR cc_start: 0.6157 (m-80) cc_final: 0.5793 (m-80) REVERT: D 169 GLN cc_start: 0.8466 (pp30) cc_final: 0.8151 (pp30) REVERT: D 240 MET cc_start: 0.5433 (tmm) cc_final: 0.5109 (tmm) REVERT: D 245 VAL cc_start: 0.5740 (OUTLIER) cc_final: 0.5480 (p) REVERT: D 300 GLN cc_start: 0.7480 (pm20) cc_final: 0.7172 (pm20) outliers start: 35 outliers final: 24 residues processed: 175 average time/residue: 0.2237 time to fit residues: 53.9754 Evaluate side-chains 175 residues out of total 957 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 146 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 219 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 148 CYS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 253 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 113 GLN Chi-restraints excluded: chain E residue 147 CYS Chi-restraints excluded: chain E residue 220 HIS Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 93 TRP Chi-restraints excluded: chain D residue 189 ILE Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 238 VAL Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 246 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.202675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.146788 restraints weight = 9638.942| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 2.38 r_work: 0.3515 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8955 Z= 0.281 Angle : 0.690 13.978 12137 Z= 0.360 Chirality : 0.045 0.282 1374 Planarity : 0.005 0.067 1530 Dihedral : 5.812 80.564 1223 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.56 % Favored : 93.35 % Rotamer: Outliers : 3.03 % Allowed : 23.30 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.26), residues: 1098 helix: 0.18 (0.28), residues: 355 sheet: -1.04 (0.32), residues: 267 loop : -1.55 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.013 0.002 HIS E 220 PHE 0.025 0.002 PHE B 253 TYR 0.029 0.002 TYR E 178 ARG 0.014 0.001 ARG E 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2341.70 seconds wall clock time: 43 minutes 1.32 seconds (2581.32 seconds total)