Starting phenix.real_space_refine on Mon Mar 11 13:07:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/03_2024/8w88_37348_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/03_2024/8w88_37348.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/03_2024/8w88_37348_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/03_2024/8w88_37348_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/03_2024/8w88_37348_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/03_2024/8w88_37348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/03_2024/8w88_37348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/03_2024/8w88_37348_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w88_37348/03_2024/8w88_37348_neut_updated.pdb" } resolution = 2.6 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= 0.001 sd= 0.131 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 5307 2.51 5 N 1419 2.21 5 O 1519 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A GLU 326": "OE1" <-> "OE2" Residue "A GLU 343": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 185": "OE1" <-> "OE2" Residue "G GLU 16": "OE1" <-> "OE2" Residue "G GLU 41": "OE1" <-> "OE2" Residue "N GLU 7": "OE1" <-> "OE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "R GLU 93": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8307 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1957 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 433 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} 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: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2254 Classifications: {'peptide': 281} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 96 Unusual residues: {'CLR': 3, 'UJL': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 4.82, per 1000 atoms: 0.58 Number of scatterers: 8307 At special positions: 0 Unit cell: (83.224, 99.704, 135.136, 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 1519 8.00 N 1419 7.00 C 5307 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.28 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: 3.19 Conformation dependent library (CDL) restraints added in 1.6 seconds 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 10 sheets defined 39.4% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 9 through 36 removed outlier: 3.558A pdb=" N LYS A 31 " --> pdb=" O LYS A 27 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 59 Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 264 through 277 Processing helix chain 'A' and resid 293 through 301 Processing helix chain 'A' and resid 307 through 310 No H-bonds generated for 'chain 'A' and resid 307 through 310' Processing helix chain 'A' and resid 312 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.506A pdb=" N PHE A 344 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 389 Processing helix chain 'B' and resid 18 through 38 Processing helix chain 'B' and resid 43 through 49 removed outlier: 4.692A pdb=" N ASN B 49 " --> pdb=" O GLN B 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 22 Processing helix chain 'G' and resid 29 through 42 Processing helix chain 'N' and resid 30 through 32 No H-bonds generated for 'chain 'N' and resid 30 through 32' Processing helix chain 'N' and resid 89 through 91 No H-bonds generated for 'chain 'N' and resid 89 through 91' Processing helix chain 'R' and resid 20 through 50 Processing helix chain 'R' and resid 57 through 75 Processing helix chain 'R' and resid 77 through 85 Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.685A pdb=" N LYS R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 removed outlier: 3.586A pdb=" N TYR R 131 " --> pdb=" O PRO R 128 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N LYS R 132 " --> pdb=" O LEU R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 159 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 178 removed outlier: 3.740A pdb=" N HIS R 177 " --> pdb=" O TYR R 173 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 228 Processing helix chain 'R' and resid 248 through 276 removed outlier: 3.683A pdb=" N PHE R 260 " --> pdb=" O VAL R 256 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 283 through 304 removed outlier: 3.722A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 315 removed outlier: 3.514A pdb=" N ALA R 314 " --> pdb=" O TRP R 310 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 358 through 362 removed outlier: 7.139A pdb=" N VAL A 286 " --> pdb=" O TYR A 359 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N HIS A 361 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU A 288 " --> pdb=" O HIS A 361 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA A 242 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASN A 217 " --> pdb=" O HIS A 40 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N LEU A 42 " --> pdb=" O ASN A 217 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N HIS A 219 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N LEU A 44 " --> pdb=" O HIS A 219 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE A 221 " --> pdb=" O LEU A 44 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 71 through 76 removed outlier: 6.807A pdb=" N ALA B 86 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N MET B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 84 " --> pdb=" O MET B 74 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N TRP B 76 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU B 82 " --> pdb=" O TRP B 76 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP B 96 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.917A pdb=" N LYS B 102 " --> pdb=" O ASP B 96 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 113 through 118 removed outlier: 6.657A pdb=" N GLY B 128 " --> pdb=" O MET B 114 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N CYS B 116 " --> pdb=" O ALA B 126 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N ALA B 126 " --> pdb=" O CYS B 116 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N TYR B 118 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N TYR B 124 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASN B 138 " --> pdb=" O VAL B 148 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N VAL B 148 " --> pdb=" O ASN B 138 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 159 through 164 removed outlier: 6.593A pdb=" N SER B 173 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N CYS B 162 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 171 " --> pdb=" O CYS B 162 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N PHE B 164 " --> pdb=" O GLN B 169 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N GLN B 169 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE B 170 " --> pdb=" O TRP B 182 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 183 " --> pdb=" O GLN B 189 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN B 189 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 200 through 205 removed outlier: 6.786A pdb=" N GLY B 215 " --> pdb=" O MET B 201 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU B 203 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 213 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N LEU B 205 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N LEU B 211 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLN B 233 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ASP B 225 " --> pdb=" O CYS B 231 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N CYS B 231 " --> pdb=" O ASP B 225 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 242 through 247 removed outlier: 6.637A pdb=" N GLY B 257 " --> pdb=" O ASN B 243 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ILE B 245 " --> pdb=" O ALA B 255 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ALA B 255 " --> pdb=" O ILE B 245 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N PHE B 247 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ALA B 253 " --> pdb=" O PHE B 247 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 275 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ASP B 267 " --> pdb=" O GLU B 273 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N GLU B 273 " --> pdb=" O ASP B 267 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 286 through 291 removed outlier: 6.383A pdb=" N GLY B 301 " --> pdb=" O THR B 287 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL B 289 " --> pdb=" O LEU B 299 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU B 299 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE B 291 " --> pdb=" O LEU B 297 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 297 " --> pdb=" O PHE B 291 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASP B 311 " --> pdb=" O ARG B 317 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG B 317 " --> pdb=" O ASP B 311 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 59 through 64 removed outlier: 3.586A pdb=" N ARG B 59 " --> pdb=" O ASN B 353 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE B 351 " --> pdb=" O ARG B 61 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N THR B 63 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU B 349 " --> pdb=" O THR B 63 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N CYS B 330 " --> pdb=" O GLY B 343 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 4 through 8 removed outlier: 3.522A pdb=" N THR N 79 " --> pdb=" O ASP N 74 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 11 through 13 removed outlier: 6.245A pdb=" N ARG N 39 " --> pdb=" O TRP N 48 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N TRP N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ALA N 41 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU N 46 " --> pdb=" O ALA N 41 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1143 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: 2.82 Time building geometry restraints manager: 3.45 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: 2655 1.34 - 1.46: 1381 1.46 - 1.57: 4369 1.57 - 1.69: 1 1.69 - 1.81: 88 Bond restraints: 8494 Sorted by residual: bond pdb=" N GLU B 16 " pdb=" CA GLU B 16 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.03e+00 bond pdb=" N ASN G 4 " pdb=" CA ASN G 4 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.92e+00 bond pdb=" CA LYS R 313 " pdb=" CB LYS R 313 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.55e-02 4.16e+03 2.74e+00 bond pdb=" N THR A 8 " pdb=" CA THR A 8 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.70e+00 bond pdb=" C3 UJL R 404 " pdb=" O1 UJL R 404 " ideal model delta sigma weight residual 1.460 1.427 0.033 2.00e-02 2.50e+03 2.65e+00 ... (remaining 8489 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.39: 191 106.39 - 113.31: 4624 113.31 - 120.24: 3110 120.24 - 127.16: 3499 127.16 - 134.09: 94 Bond angle restraints: 11518 Sorted by residual: angle pdb=" N HIS B 238 " pdb=" CA HIS B 238 " pdb=" C HIS B 238 " ideal model delta sigma weight residual 110.43 116.41 -5.98 1.31e+00 5.83e-01 2.08e+01 angle pdb=" CA PRO N 89 " pdb=" N PRO N 89 " pdb=" CD PRO N 89 " ideal model delta sigma weight residual 112.00 107.65 4.35 1.40e+00 5.10e-01 9.67e+00 angle pdb=" CA TRP R 291 " pdb=" CB TRP R 291 " pdb=" CG TRP R 291 " ideal model delta sigma weight residual 113.60 108.78 4.82 1.90e+00 2.77e-01 6.43e+00 angle pdb=" CB LYS A 27 " pdb=" CG LYS A 27 " pdb=" CD LYS A 27 " ideal model delta sigma weight residual 111.30 116.88 -5.58 2.30e+00 1.89e-01 5.89e+00 angle pdb=" N VAL R 150 " pdb=" CA VAL R 150 " pdb=" C VAL R 150 " ideal model delta sigma weight residual 112.35 109.56 2.79 1.20e+00 6.94e-01 5.41e+00 ... (remaining 11513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 4646 17.21 - 34.43: 402 34.43 - 51.64: 100 51.64 - 68.85: 22 68.85 - 86.06: 15 Dihedral angle restraints: 5185 sinusoidal: 2159 harmonic: 3026 Sorted by residual: dihedral pdb=" CA LYS A 306 " pdb=" C LYS A 306 " pdb=" N ILE A 307 " pdb=" CA ILE A 307 " ideal model delta harmonic sigma weight residual -180.00 -161.24 -18.76 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA TRP B 95 " pdb=" C TRP B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta harmonic sigma weight residual 180.00 162.04 17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ILE A 307 " pdb=" C ILE A 307 " pdb=" N GLU A 308 " pdb=" CA GLU A 308 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 5182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 966 0.043 - 0.086: 251 0.086 - 0.129: 70 0.129 - 0.172: 6 0.172 - 0.215: 2 Chirality restraints: 1295 Sorted by residual: chirality pdb=" CA ASN R 41 " pdb=" N ASN R 41 " pdb=" C ASN R 41 " pdb=" CB ASN R 41 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA HIS B 238 " pdb=" N HIS B 238 " pdb=" C HIS B 238 " pdb=" CB HIS B 238 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.69e-01 chirality pdb=" CA ILE R 281 " pdb=" N ILE R 281 " pdb=" C ILE R 281 " pdb=" CB ILE R 281 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 1292 not shown) Planarity restraints: 1446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 88 " 0.051 5.00e-02 4.00e+02 7.59e-02 9.21e+00 pdb=" N PRO N 89 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO N 89 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO N 89 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG N 106 " 0.248 9.50e-02 1.11e+02 1.12e-01 8.65e+00 pdb=" NE ARG N 106 " -0.021 2.00e-02 2.50e+03 pdb=" CZ ARG N 106 " 0.015 2.00e-02 2.50e+03 pdb=" NH1 ARG N 106 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG N 106 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 264 " -0.130 9.50e-02 1.11e+02 5.86e-02 2.20e+00 pdb=" NE ARG A 264 " 0.010 2.00e-02 2.50e+03 pdb=" CZ ARG A 264 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 264 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 264 " -0.003 2.00e-02 2.50e+03 ... (remaining 1443 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 207 2.69 - 3.25: 8188 3.25 - 3.80: 13367 3.80 - 4.35: 18610 4.35 - 4.90: 31078 Nonbonded interactions: 71450 Sorted by model distance: nonbonded pdb=" N GLU A 326 " pdb=" OE1 GLU A 326 " model vdw 2.143 2.520 nonbonded pdb=" OG SER B 294 " pdb=" OD2 ASP G 47 " model vdw 2.210 2.440 nonbonded pdb=" OH TYR A 317 " pdb=" OD2 ASP A 342 " model vdw 2.229 2.440 nonbonded pdb=" O PHE R 145 " pdb=" OG SER R 149 " model vdw 2.231 2.440 nonbonded pdb=" O ASP B 208 " pdb=" OG1 THR B 209 " model vdw 2.266 2.440 ... (remaining 71445 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=0.01 max=1.00 mean=0.94 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: 0.700 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: 4.050 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.520 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 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 : 0.005 0.061 8494 Z= 0.301 Angle : 0.591 5.981 11518 Z= 0.333 Chirality : 0.042 0.215 1295 Planarity : 0.005 0.112 1446 Dihedral : 14.739 86.062 3226 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.34 % Allowed : 14.77 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1023 helix: 2.06 (0.26), residues: 409 sheet: 0.04 (0.34), residues: 216 loop : -0.39 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 291 HIS 0.004 0.001 HIS B 67 PHE 0.014 0.002 PHE R 160 TYR 0.013 0.001 TYR R 304 ARG 0.018 0.001 ARG N 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: A 326 GLU cc_start: 0.6524 (mp0) cc_final: 0.6294 (tp30) REVERT: B 72 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: N 47 GLU cc_start: 0.8111 (tt0) cc_final: 0.7891 (tt0) outliers start: 3 outliers final: 2 residues processed: 130 average time/residue: 1.3654 time to fit residues: 187.9305 Evaluate side-chains 117 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 114 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 287 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 34 GLN B 189 GLN B 238 HIS B 272 GLN N 4 GLN N 6 GLN R 296 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8494 Z= 0.188 Angle : 0.512 6.076 11518 Z= 0.274 Chirality : 0.043 0.141 1295 Planarity : 0.004 0.049 1446 Dihedral : 5.286 58.948 1338 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.91 % Allowed : 13.76 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1023 helix: 2.29 (0.26), residues: 409 sheet: 0.02 (0.34), residues: 230 loop : -0.19 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 95 HIS 0.003 0.001 HIS B 67 PHE 0.014 0.001 PHE R 160 TYR 0.014 0.001 TYR R 79 ARG 0.005 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 126 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 295 LEU cc_start: 0.8274 (mp) cc_final: 0.7983 (tp) REVERT: A 316 ARG cc_start: 0.7305 (OUTLIER) cc_final: 0.6951 (ptt90) REVERT: B 72 TYR cc_start: 0.9073 (OUTLIER) cc_final: 0.7896 (m-80) REVERT: B 83 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8511 (pp) REVERT: B 247 PHE cc_start: 0.9201 (OUTLIER) cc_final: 0.8156 (t80) outliers start: 26 outliers final: 10 residues processed: 143 average time/residue: 1.2481 time to fit residues: 190.3283 Evaluate side-chains 130 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.0050 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 5.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 272 GLN N 4 GLN N 6 GLN N 32 ASN R 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8494 Z= 0.211 Angle : 0.506 6.263 11518 Z= 0.270 Chirality : 0.043 0.135 1295 Planarity : 0.004 0.050 1446 Dihedral : 5.186 56.508 1338 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.36 % Allowed : 14.65 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.27), residues: 1023 helix: 2.34 (0.26), residues: 410 sheet: -0.04 (0.34), residues: 230 loop : -0.13 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 291 HIS 0.003 0.001 HIS R 63 PHE 0.014 0.001 PHE R 160 TYR 0.013 0.001 TYR R 79 ARG 0.006 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 114 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8677 (tt0) REVERT: A 295 LEU cc_start: 0.8324 (mp) cc_final: 0.8056 (tp) REVERT: A 316 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6947 (ptt90) REVERT: B 72 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: B 83 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8606 (pp) REVERT: R 53 GLN cc_start: 0.7611 (OUTLIER) cc_final: 0.7166 (pm20) outliers start: 30 outliers final: 14 residues processed: 134 average time/residue: 1.2244 time to fit residues: 174.7524 Evaluate side-chains 130 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 111 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 287 THR Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 53 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 9.9990 chunk 47 optimal weight: 0.0970 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN N 4 GLN N 6 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 8494 Z= 0.235 Angle : 0.510 6.088 11518 Z= 0.272 Chirality : 0.043 0.160 1295 Planarity : 0.004 0.051 1446 Dihedral : 5.162 56.006 1338 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 4.03 % Allowed : 14.88 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1023 helix: 2.29 (0.26), residues: 410 sheet: -0.13 (0.33), residues: 227 loop : -0.13 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.004 0.001 HIS R 63 PHE 0.015 0.002 PHE R 160 TYR 0.017 0.001 TYR R 79 ARG 0.007 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 111 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8637 (tt0) REVERT: A 295 LEU cc_start: 0.8369 (mp) cc_final: 0.8118 (tp) REVERT: A 316 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6947 (ptt90) REVERT: B 72 TYR cc_start: 0.9061 (OUTLIER) cc_final: 0.7940 (m-80) REVERT: B 83 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8636 (pp) REVERT: R 53 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7137 (pm20) outliers start: 36 outliers final: 17 residues processed: 135 average time/residue: 1.1552 time to fit residues: 166.2534 Evaluate side-chains 130 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 108 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 209 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 272 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8494 Z= 0.225 Angle : 0.507 8.978 11518 Z= 0.268 Chirality : 0.043 0.154 1295 Planarity : 0.004 0.053 1446 Dihedral : 4.979 56.091 1337 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.69 % Allowed : 15.21 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1023 helix: 2.32 (0.26), residues: 410 sheet: -0.16 (0.33), residues: 227 loop : -0.14 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.004 0.001 HIS R 63 PHE 0.013 0.001 PHE R 160 TYR 0.014 0.001 TYR R 79 ARG 0.006 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 111 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8638 (tt0) REVERT: A 295 LEU cc_start: 0.8398 (mp) cc_final: 0.8154 (tp) REVERT: A 316 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6962 (ptt90) REVERT: B 72 TYR cc_start: 0.9072 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: B 83 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8628 (pp) REVERT: R 53 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7123 (pm20) REVERT: R 193 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8247 (mm) outliers start: 33 outliers final: 18 residues processed: 135 average time/residue: 1.2533 time to fit residues: 180.1419 Evaluate side-chains 132 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 108 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 111 SER Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 209 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 7.9990 chunk 19 optimal weight: 0.0980 chunk 57 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 272 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8494 Z= 0.148 Angle : 0.461 8.582 11518 Z= 0.244 Chirality : 0.041 0.133 1295 Planarity : 0.004 0.054 1446 Dihedral : 4.688 56.795 1337 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.47 % Allowed : 16.33 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.27), residues: 1023 helix: 2.44 (0.26), residues: 410 sheet: -0.17 (0.33), residues: 225 loop : -0.14 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 291 HIS 0.002 0.001 HIS R 63 PHE 0.010 0.001 PHE B 164 TYR 0.015 0.001 TYR N 61 ARG 0.007 0.000 ARG A 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 116 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8816 (OUTLIER) cc_final: 0.8554 (tt0) REVERT: A 295 LEU cc_start: 0.8363 (mp) cc_final: 0.8122 (tp) REVERT: A 316 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.6927 (ptt90) REVERT: B 72 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.7851 (m-80) REVERT: B 83 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8494 (pp) REVERT: R 53 GLN cc_start: 0.7548 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: R 193 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8257 (mm) outliers start: 31 outliers final: 18 residues processed: 137 average time/residue: 1.1812 time to fit residues: 172.4699 Evaluate side-chains 134 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain G residue 28 LYS Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 92 THR Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 53 GLN Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 209 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 71 optimal weight: 0.0170 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 272 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8494 Z= 0.136 Angle : 0.450 8.132 11518 Z= 0.237 Chirality : 0.040 0.132 1295 Planarity : 0.004 0.056 1446 Dihedral : 4.456 57.466 1335 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.02 % Allowed : 17.00 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.27), residues: 1023 helix: 2.57 (0.26), residues: 410 sheet: -0.19 (0.32), residues: 225 loop : -0.10 (0.32), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 291 HIS 0.002 0.000 HIS R 63 PHE 0.011 0.001 PHE R 51 TYR 0.016 0.001 TYR N 61 ARG 0.006 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8574 (tt0) REVERT: A 295 LEU cc_start: 0.8337 (mp) cc_final: 0.8103 (tp) REVERT: A 316 ARG cc_start: 0.7295 (OUTLIER) cc_final: 0.6916 (ptt90) REVERT: B 72 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.7813 (m-80) REVERT: B 83 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8449 (pp) REVERT: R 193 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8282 (mm) outliers start: 27 outliers final: 15 residues processed: 134 average time/residue: 1.2070 time to fit residues: 172.6486 Evaluate side-chains 132 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain R residue 32 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 209 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 chunk 66 optimal weight: 0.0570 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 272 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8494 Z= 0.152 Angle : 0.464 7.815 11518 Z= 0.246 Chirality : 0.041 0.131 1295 Planarity : 0.004 0.054 1446 Dihedral : 4.500 57.871 1335 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.68 % Allowed : 17.67 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.27), residues: 1023 helix: 2.55 (0.26), residues: 411 sheet: -0.14 (0.32), residues: 225 loop : -0.08 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 291 HIS 0.003 0.001 HIS R 63 PHE 0.012 0.001 PHE R 51 TYR 0.017 0.001 TYR N 61 ARG 0.006 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 58 GLN cc_start: 0.7657 (mm110) cc_final: 0.6697 (tt0) REVERT: A 212 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8539 (tt0) REVERT: A 295 LEU cc_start: 0.8339 (mp) cc_final: 0.8106 (tp) REVERT: A 316 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6904 (ptt90) REVERT: B 72 TYR cc_start: 0.9094 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: B 83 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8506 (pp) REVERT: R 193 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8283 (mm) outliers start: 24 outliers final: 15 residues processed: 126 average time/residue: 1.2433 time to fit residues: 166.6239 Evaluate side-chains 131 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 111 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 209 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.8980 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 0.5980 chunk 71 optimal weight: 0.0570 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 272 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8494 Z= 0.144 Angle : 0.457 7.645 11518 Z= 0.241 Chirality : 0.040 0.131 1295 Planarity : 0.004 0.053 1446 Dihedral : 4.461 58.446 1335 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.57 % Allowed : 17.79 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 1023 helix: 2.69 (0.26), residues: 405 sheet: -0.09 (0.32), residues: 223 loop : -0.03 (0.33), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 291 HIS 0.003 0.000 HIS R 63 PHE 0.013 0.001 PHE R 51 TYR 0.016 0.001 TYR N 61 ARG 0.007 0.000 ARG A 264 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 112 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8779 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: A 295 LEU cc_start: 0.8328 (mp) cc_final: 0.8100 (tp) REVERT: A 316 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6899 (ptt90) REVERT: B 72 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.7911 (m-80) REVERT: B 83 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8494 (pp) REVERT: B 247 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8237 (t80) REVERT: R 193 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8283 (mm) outliers start: 23 outliers final: 16 residues processed: 127 average time/residue: 1.2366 time to fit residues: 167.1588 Evaluate side-chains 133 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 100 optimal weight: 0.0980 chunk 92 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.3980 chunk 61 optimal weight: 0.0980 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8494 Z= 0.127 Angle : 0.448 7.582 11518 Z= 0.237 Chirality : 0.040 0.131 1295 Planarity : 0.004 0.054 1446 Dihedral : 4.384 59.484 1335 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.13 % Allowed : 18.34 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 1023 helix: 2.66 (0.26), residues: 407 sheet: -0.08 (0.32), residues: 227 loop : 0.10 (0.33), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 291 HIS 0.002 0.000 HIS R 63 PHE 0.015 0.001 PHE R 51 TYR 0.016 0.001 TYR N 61 ARG 0.007 0.000 ARG A 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2046 Ramachandran restraints generated. 1023 Oldfield, 0 Emsley, 1023 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 119 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 212 GLN cc_start: 0.8701 (OUTLIER) cc_final: 0.8474 (tt0) REVERT: A 295 LEU cc_start: 0.8320 (mp) cc_final: 0.8078 (tp) REVERT: A 316 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6890 (ptt90) REVERT: B 72 TYR cc_start: 0.9103 (OUTLIER) cc_final: 0.7947 (m-80) REVERT: B 247 PHE cc_start: 0.9150 (OUTLIER) cc_final: 0.8226 (t80) REVERT: N 84 MET cc_start: 0.7988 (ptm) cc_final: 0.7772 (mtp) REVERT: R 193 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8326 (mm) outliers start: 19 outliers final: 13 residues processed: 131 average time/residue: 1.1725 time to fit residues: 163.9622 Evaluate side-chains 130 residues out of total 899 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 GLN Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 316 ARG Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain B residue 72 TYR Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 116 CYS Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 191 THR Chi-restraints excluded: chain B residue 247 PHE Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 330 CYS Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 105 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 115 THR Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 209 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.0770 chunk 70 optimal weight: 10.0000 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 233 GLN B 272 GLN N 4 GLN N 6 GLN N 78 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.157299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.122359 restraints weight = 9486.730| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.81 r_work: 0.3471 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3382 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3382 r_free = 0.3382 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 47 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3336 r_free = 0.3336 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 79 | |-----------------------------------------------------------------------------| r_final: 0.3336 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8494 Z= 0.140 Angle : 0.454 7.469 11518 Z= 0.240 Chirality : 0.040 0.131 1295 Planarity : 0.004 0.053 1446 Dihedral : 4.404 59.478 1335 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.24 % Allowed : 19.13 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.27), residues: 1023 helix: 2.71 (0.26), residues: 405 sheet: -0.08 (0.32), residues: 225 loop : 0.08 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP R 291 HIS 0.003 0.000 HIS R 63 PHE 0.015 0.001 PHE R 51 TYR 0.016 0.001 TYR N 61 ARG 0.007 0.000 ARG A 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3573.79 seconds wall clock time: 64 minutes 11.31 seconds (3851.31 seconds total)