Starting phenix.real_space_refine on Tue Feb 13 22:57:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/02_2024/7xtq_33452_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/02_2024/7xtq_33452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/02_2024/7xtq_33452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/02_2024/7xtq_33452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/02_2024/7xtq_33452_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xtq_33452/02_2024/7xtq_33452_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 46 5.16 5 Cl 2 4.86 5 C 5066 2.51 5 N 1420 2.21 5 O 1476 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 109": "OD1" <-> "OD2" Residue "R PHE 233": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8010 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1897 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "C" Number of residues, atoms: 229, 1886 Classifications: {'peptide': 229} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1910 Chain: "B" Number of atoms: 2612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2612 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2090 Unusual residues: {'H8I': 1} Classifications: {'peptide': 273, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 21, 'TRANS': 251, None: 1} Not linked: pdbres="ARG R 292 " pdbres="H8I R 401 " Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 380 " occ=0.50 ... (20 atoms not shown) pdb=" NH2CARG A 380 " occ=0.62 Time building chain proxies: 5.76, per 1000 atoms: 0.72 Number of scatterers: 8010 At special positions: 0 Unit cell: (77.064, 114.582, 122.694, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 46 16.00 O 1476 8.00 N 1420 7.00 C 5066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 155 " 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: 2.87 Conformation dependent library (CDL) restraints added in 1.9 seconds 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 25 helices and 10 sheets defined 37.1% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 removed outlier: 4.409A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.732A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 2 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 6 through 22 Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.423A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.936A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 21 through 41 Processing helix chain 'R' and resid 45 through 47 No H-bonds generated for 'chain 'R' and resid 45 through 47' Processing helix chain 'R' and resid 49 through 66 Processing helix chain 'R' and resid 68 through 74 Proline residue: R 72 - end of helix Processing helix chain 'R' and resid 82 through 115 Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 124 through 144 removed outlier: 3.673A pdb=" N GLY R 134 " --> pdb=" O LEU R 130 " (cutoff:3.500A) Proline residue: R 135 - end of helix Proline residue: R 142 - end of helix Processing helix chain 'R' and resid 157 through 160 No H-bonds generated for 'chain 'R' and resid 157 through 160' Processing helix chain 'R' and resid 163 through 173 Processing helix chain 'R' and resid 175 through 206 removed outlier: 3.732A pdb=" N LEU R 202 " --> pdb=" O ASP R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 251 removed outlier: 4.603A pdb=" N GLY R 238 " --> pdb=" O GLY R 234 " (cutoff:3.500A) Proline residue: R 239 - end of helix Processing helix chain 'R' and resid 262 through 281 Proline residue: R 277 - end of helix Processing helix chain 'R' and resid 285 through 288 No H-bonds generated for 'chain 'R' and resid 285 through 288' Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.076A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 46 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.194A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLY A 47 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N VAL A 224 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.013A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.858A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.672A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.955A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.765A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.040A 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 removed outlier: 3.657A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.929A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.621A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.577A pdb=" N MET N 34 " --> pdb=" O ILE N 51 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1069 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: 2.18 Time building geometry restraints manager: 3.14 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: 2581 1.34 - 1.45: 1237 1.45 - 1.57: 4298 1.57 - 1.69: 0 1.69 - 1.81: 65 Bond restraints: 8181 Sorted by residual: bond pdb=" C1 H8I R 401 " pdb=" N2 H8I R 401 " ideal model delta sigma weight residual 1.352 1.407 -0.055 2.00e-02 2.50e+03 7.51e+00 bond pdb=" C3 H8I R 401 " pdb=" N1 H8I R 401 " ideal model delta sigma weight residual 1.309 1.355 -0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" C7 H8I R 401 " pdb=" O1 H8I R 401 " ideal model delta sigma weight residual 1.365 1.403 -0.038 2.00e-02 2.50e+03 3.70e+00 bond pdb=" C7 H8I R 401 " pdb=" C8 H8I R 401 " ideal model delta sigma weight residual 1.390 1.424 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" C2 H8I R 401 " pdb=" C3 H8I R 401 " ideal model delta sigma weight residual 1.396 1.424 -0.028 2.00e-02 2.50e+03 2.02e+00 ... (remaining 8176 not shown) Histogram of bond angle deviations from ideal: 99.99 - 106.80: 217 106.80 - 113.60: 4411 113.60 - 120.40: 3135 120.40 - 127.21: 3241 127.21 - 134.01: 103 Bond angle restraints: 11107 Sorted by residual: angle pdb=" C2 H8I R 401 " pdb=" C1 H8I R 401 " pdb=" N2 H8I R 401 " ideal model delta sigma weight residual 117.71 131.52 -13.81 3.00e+00 1.11e-01 2.12e+01 angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 109.63 3.57 9.60e-01 1.09e+00 1.39e+01 angle pdb=" N GLN B 9 " pdb=" CA GLN B 9 " pdb=" CB GLN B 9 " ideal model delta sigma weight residual 110.28 115.61 -5.33 1.55e+00 4.16e-01 1.18e+01 angle pdb=" C3 H8I R 401 " pdb=" O1 H8I R 401 " pdb=" C7 H8I R 401 " ideal model delta sigma weight residual 119.25 129.24 -9.99 3.00e+00 1.11e-01 1.11e+01 angle pdb=" C PRO A 321 " pdb=" N GLU A 322 " pdb=" CA GLU A 322 " ideal model delta sigma weight residual 121.54 127.76 -6.22 1.91e+00 2.74e-01 1.06e+01 ... (remaining 11102 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 4501 17.64 - 35.28: 326 35.28 - 52.92: 51 52.92 - 70.55: 9 70.55 - 88.19: 4 Dihedral angle restraints: 4891 sinusoidal: 1920 harmonic: 2971 Sorted by residual: dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 50.97 42.03 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA PHE B 234 " pdb=" C PHE B 234 " pdb=" N PHE B 235 " pdb=" CA PHE B 235 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA PRO B 194 " pdb=" C PRO B 194 " pdb=" N ASP B 195 " pdb=" CA ASP B 195 " ideal model delta harmonic sigma weight residual 180.00 164.07 15.93 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 4888 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 796 0.037 - 0.074: 307 0.074 - 0.111: 112 0.111 - 0.148: 22 0.148 - 0.185: 5 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA GLN A 31 " pdb=" N GLN A 31 " pdb=" C GLN A 31 " pdb=" CB GLN A 31 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.60e-01 chirality pdb=" CB THR B 223 " pdb=" CA THR B 223 " pdb=" OG1 THR B 223 " pdb=" CG2 THR B 223 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.59e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.46e-01 ... (remaining 1239 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY R 134 " 0.036 5.00e-02 4.00e+02 5.50e-02 4.85e+00 pdb=" N PRO R 135 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO R 135 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 135 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 228 " -0.181 9.50e-02 1.11e+02 8.14e-02 4.28e+00 pdb=" NE ARG A 228 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 228 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG A 228 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 228 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 320 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO A 321 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " -0.026 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 473 2.73 - 3.27: 7797 3.27 - 3.82: 13099 3.82 - 4.36: 14802 4.36 - 4.90: 26442 Nonbonded interactions: 62613 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.192 2.440 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.194 2.440 nonbonded pdb=" O MET B 325 " pdb=" OD1 ASN B 340 " model vdw 2.214 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.246 2.440 nonbonded pdb=" O GLN B 75 " pdb=" OG SER B 98 " model vdw 2.273 2.440 ... (remaining 62608 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.38 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: 0.430 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: 0.000 Extract box with map and model: 1.970 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.230 Find NCS groups from input model: 0.220 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8181 Z= 0.243 Angle : 0.745 13.809 11107 Z= 0.371 Chirality : 0.046 0.185 1242 Planarity : 0.005 0.081 1431 Dihedral : 12.535 88.193 2966 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.26), residues: 1016 helix: 1.49 (0.25), residues: 399 sheet: -0.69 (0.34), residues: 215 loop : -1.79 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 281 HIS 0.007 0.001 HIS A 220 PHE 0.023 0.002 PHE A 212 TYR 0.014 0.001 TYR B 59 ARG 0.008 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 205 time to evaluate : 0.950 Fit side-chains REVERT: A 21 GLU cc_start: 0.6377 (mm-30) cc_final: 0.6096 (mm-30) REVERT: A 209 GLU cc_start: 0.6027 (tp30) cc_final: 0.5750 (tp30) REVERT: A 210 THR cc_start: 0.8203 (p) cc_final: 0.7399 (m) REVERT: A 228 ARG cc_start: 0.7563 (ptm-80) cc_final: 0.7231 (ptt180) REVERT: A 299 GLU cc_start: 0.7339 (tp30) cc_final: 0.6947 (tp30) REVERT: A 392 GLU cc_start: 0.7115 (tp30) cc_final: 0.6546 (tp30) REVERT: B 83 ASP cc_start: 0.7800 (t0) cc_final: 0.7335 (t70) REVERT: B 148 CYS cc_start: 0.7185 (t) cc_final: 0.6952 (t) REVERT: B 170 ASP cc_start: 0.6873 (t0) cc_final: 0.6569 (t0) REVERT: B 197 ARG cc_start: 0.7076 (mtp180) cc_final: 0.6439 (mtp180) REVERT: B 214 ARG cc_start: 0.7301 (ptt90) cc_final: 0.6357 (ptt90) REVERT: G 21 MET cc_start: 0.6969 (tmm) cc_final: 0.6692 (tmm) REVERT: N 31 ASN cc_start: 0.8264 (m110) cc_final: 0.8024 (m110) REVERT: N 43 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7855 (mmmt) REVERT: R 248 VAL cc_start: 0.7218 (t) cc_final: 0.6969 (t) outliers start: 0 outliers final: 0 residues processed: 205 average time/residue: 0.2766 time to fit residues: 71.0001 Evaluate side-chains 181 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 10.0000 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 213 GLN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8181 Z= 0.217 Angle : 0.608 10.522 11107 Z= 0.290 Chirality : 0.043 0.173 1242 Planarity : 0.004 0.050 1431 Dihedral : 5.083 64.653 1145 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.18 % Allowed : 9.60 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1016 helix: 2.00 (0.26), residues: 392 sheet: -0.39 (0.33), residues: 210 loop : -1.71 (0.28), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 PHE 0.016 0.001 PHE N 108 TYR 0.014 0.001 TYR N 60 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 187 time to evaluate : 0.905 Fit side-chains REVERT: A 21 GLU cc_start: 0.6386 (mm-30) cc_final: 0.6073 (mm-30) REVERT: A 209 GLU cc_start: 0.6217 (tp30) cc_final: 0.5855 (tp30) REVERT: A 299 GLU cc_start: 0.7391 (tp30) cc_final: 0.6937 (tp30) REVERT: A 392 GLU cc_start: 0.7110 (tp30) cc_final: 0.6827 (tp30) REVERT: B 127 LYS cc_start: 0.7874 (mptt) cc_final: 0.7660 (mptt) REVERT: B 148 CYS cc_start: 0.7183 (t) cc_final: 0.6950 (t) REVERT: B 197 ARG cc_start: 0.7006 (mtp180) cc_final: 0.6631 (mtp180) REVERT: B 214 ARG cc_start: 0.7272 (ptt90) cc_final: 0.6386 (ptt90) REVERT: B 295 ASN cc_start: 0.7973 (m-40) cc_final: 0.7736 (m-40) REVERT: G 21 MET cc_start: 0.6956 (tmm) cc_final: 0.6744 (tmm) REVERT: N 31 ASN cc_start: 0.8276 (m110) cc_final: 0.8053 (m110) REVERT: N 43 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7878 (mmmt) REVERT: N 60 TYR cc_start: 0.8421 (m-80) cc_final: 0.7978 (m-80) REVERT: R 80 ARG cc_start: 0.6978 (ttm-80) cc_final: 0.6711 (ttm-80) outliers start: 10 outliers final: 6 residues processed: 191 average time/residue: 0.2774 time to fit residues: 67.5607 Evaluate side-chains 190 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 184 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 0.0040 chunk 72 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8181 Z= 0.168 Angle : 0.567 8.983 11107 Z= 0.267 Chirality : 0.041 0.163 1242 Planarity : 0.004 0.048 1431 Dihedral : 4.775 64.537 1145 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.30 % Allowed : 12.44 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.26), residues: 1016 helix: 2.24 (0.27), residues: 393 sheet: -0.42 (0.33), residues: 220 loop : -1.53 (0.29), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.012 0.001 PHE N 108 TYR 0.009 0.001 TYR A 339 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 189 time to evaluate : 0.935 Fit side-chains REVERT: A 21 GLU cc_start: 0.6340 (mm-30) cc_final: 0.6009 (mm-30) REVERT: A 209 GLU cc_start: 0.6267 (tp30) cc_final: 0.5878 (tp30) REVERT: A 299 GLU cc_start: 0.7400 (tp30) cc_final: 0.6924 (tp30) REVERT: A 392 GLU cc_start: 0.7036 (tp30) cc_final: 0.6782 (tp30) REVERT: B 126 LEU cc_start: 0.8085 (mm) cc_final: 0.7805 (mp) REVERT: B 148 CYS cc_start: 0.7179 (t) cc_final: 0.6929 (t) REVERT: B 197 ARG cc_start: 0.6946 (mtp180) cc_final: 0.6525 (mtp180) REVERT: B 214 ARG cc_start: 0.7288 (ptt90) cc_final: 0.6685 (ptt90) REVERT: B 234 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.8037 (m-80) REVERT: B 295 ASN cc_start: 0.8006 (m-40) cc_final: 0.7781 (m-40) REVERT: G 21 MET cc_start: 0.6968 (tmm) cc_final: 0.6748 (tmm) REVERT: N 43 LYS cc_start: 0.8201 (mmmt) cc_final: 0.7879 (mmmt) outliers start: 11 outliers final: 6 residues processed: 192 average time/residue: 0.2818 time to fit residues: 67.5317 Evaluate side-chains 191 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 184 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.0040 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 54 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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** N 31 ASN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8181 Z= 0.155 Angle : 0.553 8.639 11107 Z= 0.260 Chirality : 0.041 0.167 1242 Planarity : 0.004 0.047 1431 Dihedral : 4.611 62.207 1145 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.66 % Allowed : 14.34 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.27), residues: 1016 helix: 2.38 (0.27), residues: 393 sheet: -0.32 (0.33), residues: 225 loop : -1.47 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE B 241 TYR 0.009 0.001 TYR A 339 ARG 0.005 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 0.890 Fit side-chains REVERT: A 21 GLU cc_start: 0.6334 (mm-30) cc_final: 0.6003 (mm-30) REVERT: A 209 GLU cc_start: 0.6277 (tp30) cc_final: 0.5916 (tp30) REVERT: A 210 THR cc_start: 0.7912 (p) cc_final: 0.7353 (m) REVERT: A 299 GLU cc_start: 0.7383 (tp30) cc_final: 0.6929 (tp30) REVERT: A 392 GLU cc_start: 0.7001 (tp30) cc_final: 0.6743 (tp30) REVERT: B 40 VAL cc_start: 0.8173 (OUTLIER) cc_final: 0.7821 (p) REVERT: B 126 LEU cc_start: 0.7726 (mm) cc_final: 0.7308 (mt) REVERT: B 148 CYS cc_start: 0.7146 (t) cc_final: 0.6905 (t) REVERT: B 197 ARG cc_start: 0.6910 (mtp180) cc_final: 0.6506 (mtp180) REVERT: B 214 ARG cc_start: 0.7277 (ptt90) cc_final: 0.6691 (ptt90) REVERT: B 234 PHE cc_start: 0.8312 (OUTLIER) cc_final: 0.8058 (m-80) REVERT: G 21 MET cc_start: 0.6970 (tmm) cc_final: 0.6731 (tmm) REVERT: N 43 LYS cc_start: 0.8190 (mmmt) cc_final: 0.7872 (mmmt) outliers start: 14 outliers final: 7 residues processed: 189 average time/residue: 0.2782 time to fit residues: 65.7802 Evaluate side-chains 190 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 181 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 5.9990 chunk 71 optimal weight: 0.0370 chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 0.0050 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 overall best weight: 0.4872 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN N 53 GLN R 93 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8181 Z= 0.145 Angle : 0.538 8.108 11107 Z= 0.252 Chirality : 0.040 0.149 1242 Planarity : 0.004 0.046 1431 Dihedral : 4.479 62.675 1145 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.42 % Allowed : 16.11 % Favored : 82.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.27), residues: 1016 helix: 2.46 (0.27), residues: 393 sheet: -0.23 (0.33), residues: 235 loop : -1.31 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE B 241 TYR 0.009 0.001 TYR A 339 ARG 0.005 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 185 time to evaluate : 0.830 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6319 (mm-30) cc_final: 0.5998 (mm-30) REVERT: A 209 GLU cc_start: 0.6296 (tp30) cc_final: 0.5925 (tp30) REVERT: A 210 THR cc_start: 0.7876 (p) cc_final: 0.7256 (m) REVERT: A 299 GLU cc_start: 0.7383 (tp30) cc_final: 0.6918 (tp30) REVERT: A 392 GLU cc_start: 0.7019 (tp30) cc_final: 0.6726 (tp30) REVERT: B 40 VAL cc_start: 0.8183 (OUTLIER) cc_final: 0.7843 (p) REVERT: B 61 MET cc_start: 0.7155 (ppp) cc_final: 0.6838 (ppp) REVERT: B 126 LEU cc_start: 0.7617 (mm) cc_final: 0.7297 (mt) REVERT: B 253 PHE cc_start: 0.7714 (m-80) cc_final: 0.7429 (m-80) REVERT: B 286 LEU cc_start: 0.7857 (mt) cc_final: 0.7644 (mp) REVERT: G 21 MET cc_start: 0.6892 (tmm) cc_final: 0.6660 (tmm) REVERT: N 43 LYS cc_start: 0.8188 (mmmt) cc_final: 0.7866 (mmmt) outliers start: 12 outliers final: 8 residues processed: 189 average time/residue: 0.2679 time to fit residues: 63.4766 Evaluate side-chains 194 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 185 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 0.7980 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8181 Z= 0.211 Angle : 0.564 9.536 11107 Z= 0.267 Chirality : 0.041 0.155 1242 Planarity : 0.004 0.045 1431 Dihedral : 4.595 63.159 1145 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.25 % Allowed : 16.47 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 1016 helix: 2.36 (0.27), residues: 393 sheet: -0.16 (0.33), residues: 233 loop : -1.30 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 82 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.002 PHE B 234 TYR 0.009 0.001 TYR A 339 ARG 0.005 0.000 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 0.930 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6390 (mm-30) cc_final: 0.6046 (mm-30) REVERT: A 59 GLN cc_start: 0.5571 (pp30) cc_final: 0.5167 (pp30) REVERT: A 209 GLU cc_start: 0.6310 (tp30) cc_final: 0.5936 (tp30) REVERT: A 210 THR cc_start: 0.7909 (p) cc_final: 0.7280 (m) REVERT: A 228 ARG cc_start: 0.7833 (ptm-80) cc_final: 0.7394 (ptt180) REVERT: A 299 GLU cc_start: 0.7390 (tp30) cc_final: 0.6908 (tp30) REVERT: B 40 VAL cc_start: 0.8240 (OUTLIER) cc_final: 0.7886 (p) REVERT: B 61 MET cc_start: 0.7158 (ppp) cc_final: 0.6813 (ppp) REVERT: B 126 LEU cc_start: 0.7822 (mm) cc_final: 0.7547 (mp) REVERT: N 43 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7840 (mmmt) outliers start: 19 outliers final: 12 residues processed: 195 average time/residue: 0.2725 time to fit residues: 66.5118 Evaluate side-chains 198 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 185 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8181 Z= 0.231 Angle : 0.585 9.876 11107 Z= 0.276 Chirality : 0.042 0.182 1242 Planarity : 0.004 0.047 1431 Dihedral : 4.640 63.295 1145 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.73 % Allowed : 16.82 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.27), residues: 1016 helix: 2.25 (0.26), residues: 397 sheet: -0.15 (0.33), residues: 232 loop : -1.25 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.015 0.002 PHE N 108 TYR 0.010 0.001 TYR N 95 ARG 0.007 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 186 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6410 (mm-30) cc_final: 0.6102 (mm-30) REVERT: A 59 GLN cc_start: 0.5627 (pp30) cc_final: 0.5231 (pp30) REVERT: A 209 GLU cc_start: 0.6320 (tp30) cc_final: 0.5954 (tp30) REVERT: A 210 THR cc_start: 0.7893 (p) cc_final: 0.7263 (m) REVERT: A 228 ARG cc_start: 0.7891 (ptm-80) cc_final: 0.7474 (ptt180) REVERT: A 299 GLU cc_start: 0.7405 (tp30) cc_final: 0.6899 (tp30) REVERT: B 40 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7936 (p) REVERT: B 61 MET cc_start: 0.7130 (ppp) cc_final: 0.6749 (ppp) REVERT: B 126 LEU cc_start: 0.7957 (mm) cc_final: 0.7695 (mt) REVERT: N 43 LYS cc_start: 0.8214 (mmmt) cc_final: 0.7835 (mmmt) outliers start: 23 outliers final: 19 residues processed: 196 average time/residue: 0.2798 time to fit residues: 68.4332 Evaluate side-chains 204 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 75 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 92 optimal weight: 0.0470 chunk 84 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.7680 ------------------------------------------------------------------------------- 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** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8181 Z= 0.188 Angle : 0.576 9.133 11107 Z= 0.270 Chirality : 0.041 0.152 1242 Planarity : 0.004 0.046 1431 Dihedral : 4.546 63.489 1145 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.37 % Allowed : 17.77 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.27), residues: 1016 helix: 2.33 (0.27), residues: 393 sheet: -0.11 (0.34), residues: 233 loop : -1.27 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.020 0.001 PHE B 278 TYR 0.008 0.001 TYR A 339 ARG 0.006 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 0.976 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6392 (mm-30) cc_final: 0.6083 (mm-30) REVERT: A 59 GLN cc_start: 0.5640 (pp30) cc_final: 0.5228 (pp30) REVERT: A 209 GLU cc_start: 0.6325 (tp30) cc_final: 0.5951 (tp30) REVERT: A 210 THR cc_start: 0.7887 (p) cc_final: 0.7247 (m) REVERT: A 228 ARG cc_start: 0.7860 (ptm-80) cc_final: 0.7453 (ptt180) REVERT: A 299 GLU cc_start: 0.7402 (tp30) cc_final: 0.6889 (tp30) REVERT: B 40 VAL cc_start: 0.8269 (OUTLIER) cc_final: 0.7941 (p) REVERT: B 61 MET cc_start: 0.7058 (ppp) cc_final: 0.6733 (ppp) REVERT: B 126 LEU cc_start: 0.7721 (mm) cc_final: 0.7463 (mt) REVERT: N 32 TYR cc_start: 0.8099 (m-80) cc_final: 0.7046 (m-80) REVERT: N 43 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7844 (mmmt) REVERT: R 90 LEU cc_start: 0.7050 (pp) cc_final: 0.6643 (mp) outliers start: 20 outliers final: 18 residues processed: 191 average time/residue: 0.2780 time to fit residues: 66.5911 Evaluate side-chains 201 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 182 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 129 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 0.0070 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 94 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 0.5798 ------------------------------------------------------------------------------- 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** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8181 Z= 0.164 Angle : 0.563 8.444 11107 Z= 0.263 Chirality : 0.041 0.150 1242 Planarity : 0.004 0.046 1431 Dihedral : 4.439 63.408 1145 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.49 % Allowed : 18.13 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1016 helix: 2.41 (0.27), residues: 393 sheet: -0.09 (0.34), residues: 231 loop : -1.22 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.017 0.001 PHE B 278 TYR 0.008 0.001 TYR A 339 ARG 0.005 0.000 ARG R 187 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 183 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6379 (mm-30) cc_final: 0.6071 (mm-30) REVERT: A 59 GLN cc_start: 0.5608 (pp30) cc_final: 0.5208 (pp30) REVERT: A 209 GLU cc_start: 0.6325 (tp30) cc_final: 0.5954 (tp30) REVERT: A 210 THR cc_start: 0.7890 (p) cc_final: 0.7259 (m) REVERT: A 228 ARG cc_start: 0.7825 (ptm-80) cc_final: 0.7497 (ptt180) REVERT: A 285 THR cc_start: 0.8300 (p) cc_final: 0.8084 (m) REVERT: A 299 GLU cc_start: 0.7395 (tp30) cc_final: 0.6883 (tp30) REVERT: B 40 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.7953 (p) REVERT: B 61 MET cc_start: 0.6975 (ppp) cc_final: 0.6707 (ppp) REVERT: B 126 LEU cc_start: 0.7705 (mm) cc_final: 0.7421 (mt) REVERT: N 32 TYR cc_start: 0.8071 (m-80) cc_final: 0.7020 (m-80) REVERT: N 43 LYS cc_start: 0.8235 (mmmt) cc_final: 0.7867 (mmmt) REVERT: R 90 LEU cc_start: 0.6984 (OUTLIER) cc_final: 0.6618 (mt) REVERT: R 112 MET cc_start: 0.7512 (mmt) cc_final: 0.7148 (mpp) outliers start: 21 outliers final: 17 residues processed: 191 average time/residue: 0.2866 time to fit residues: 68.3582 Evaluate side-chains 200 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 181 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 25 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 185 SER Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 8 optimal weight: 0.0970 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 84 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8181 Z= 0.194 Angle : 0.572 8.866 11107 Z= 0.269 Chirality : 0.041 0.151 1242 Planarity : 0.004 0.045 1431 Dihedral : 4.465 63.289 1145 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.37 % Allowed : 18.84 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.27), residues: 1016 helix: 2.37 (0.27), residues: 393 sheet: -0.09 (0.34), residues: 234 loop : -1.25 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 82 HIS 0.006 0.001 HIS A 220 PHE 0.018 0.001 PHE B 278 TYR 0.008 0.001 TYR A 339 ARG 0.007 0.000 ARG R 187 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2032 Ramachandran restraints generated. 1016 Oldfield, 0 Emsley, 1016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 0.844 Fit side-chains revert: symmetry clash REVERT: A 21 GLU cc_start: 0.6417 (mm-30) cc_final: 0.6109 (mm-30) REVERT: A 59 GLN cc_start: 0.5661 (pp30) cc_final: 0.5265 (pp30) REVERT: A 209 GLU cc_start: 0.6328 (tp30) cc_final: 0.5959 (tp30) REVERT: A 210 THR cc_start: 0.7909 (p) cc_final: 0.7254 (m) REVERT: A 228 ARG cc_start: 0.7856 (ptm-80) cc_final: 0.7532 (ptt180) REVERT: A 299 GLU cc_start: 0.7409 (tp30) cc_final: 0.6885 (tp30) REVERT: B 40 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7969 (p) REVERT: B 42 ARG cc_start: 0.7025 (ttm-80) cc_final: 0.6778 (ttm-80) REVERT: B 43 ILE cc_start: 0.8352 (OUTLIER) cc_final: 0.8117 (tp) REVERT: B 61 MET cc_start: 0.7020 (ppp) cc_final: 0.6718 (ppp) REVERT: B 126 LEU cc_start: 0.7748 (mm) cc_final: 0.7488 (mt) REVERT: N 43 LYS cc_start: 0.8209 (mmmt) cc_final: 0.7839 (mmmt) REVERT: R 90 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6616 (mt) outliers start: 20 outliers final: 16 residues processed: 189 average time/residue: 0.2944 time to fit residues: 69.4407 Evaluate side-chains 199 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 180 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LYS Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain R residue 34 LEU Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 90 LEU Chi-restraints excluded: chain R residue 146 TRP Chi-restraints excluded: chain R residue 170 VAL Chi-restraints excluded: chain R residue 249 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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** N 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.136316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.114466 restraints weight = 20795.867| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 3.55 r_work: 0.3237 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8181 Z= 0.185 Angle : 0.565 8.438 11107 Z= 0.266 Chirality : 0.041 0.151 1242 Planarity : 0.004 0.045 1431 Dihedral : 4.418 62.991 1145 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.61 % Allowed : 18.84 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.27), residues: 1016 helix: 2.40 (0.27), residues: 393 sheet: -0.05 (0.34), residues: 233 loop : -1.25 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 82 HIS 0.005 0.001 HIS A 220 PHE 0.015 0.001 PHE B 278 TYR 0.008 0.001 TYR A 339 ARG 0.006 0.000 ARG R 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2316.17 seconds wall clock time: 42 minutes 28.62 seconds (2548.62 seconds total)