Starting phenix.real_space_refine on Tue Sep 24 21:21:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/09_2024/6k42_9912.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/09_2024/6k42_9912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/09_2024/6k42_9912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/09_2024/6k42_9912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/09_2024/6k42_9912.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6k42_9912/09_2024/6k42_9912.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 58 5.16 5 C 5630 2.51 5 N 1510 2.21 5 O 1618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 8816 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1759 Classifications: {'peptide': 218} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2616 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "R" Number of atoms: 2201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2201 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 12, 'TRANS': 257} Chain breaks: 3 Chain: "H" Number of atoms: 1801 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 233, 1793 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 233, 1793 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 9, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 1828 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'CZX': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N LYS H 236 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS H 236 " occ=0.00 Time building chain proxies: 6.11, per 1000 atoms: 0.69 Number of scatterers: 8816 At special positions: 0 Unit cell: (112.08, 110.679, 128.892, 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 58 16.00 O 1618 8.00 N 1510 7.00 C 5630 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 164 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 147 " - pdb=" SG CYS H 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 2.09 Conformation dependent library (CDL) restraints added in 1.1 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2098 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 13 sheets defined 33.1% alpha, 17.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 4.114A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 19 " --> pdb=" O ARG A 15 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU A 23 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 30 " --> pdb=" O ASP A 26 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.653A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.871A pdb=" N LYS A 248 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 276 removed outlier: 3.823A pdb=" N GLU A 275 " --> pdb=" O LYS A 271 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 309 removed outlier: 3.527A pdb=" N ALA A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN A 304 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A 309 " --> pdb=" O CYS A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'B' and resid 3 through 19 removed outlier: 3.770A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 22 removed outlier: 4.101A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N VAL G 16 " --> pdb=" O ALA G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.612A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 29 Processing helix chain 'R' and resid 29 through 39 Processing helix chain 'R' and resid 48 through 74 removed outlier: 3.729A pdb=" N LEU R 64 " --> pdb=" O LEU R 60 " (cutoff:3.500A) Proline residue: R 67 - end of helix Processing helix chain 'R' and resid 83 through 116 removed outlier: 4.332A pdb=" N VAL R 87 " --> pdb=" O THR R 83 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N CYS R 96 " --> pdb=" O ASP R 92 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER R 99 " --> pdb=" O PHE R 95 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N VAL R 114 " --> pdb=" O ARG R 110 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ARG R 116 " --> pdb=" O TRP R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 removed outlier: 3.942A pdb=" N ASN R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER R 122 " --> pdb=" O LEU R 118 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 117 through 122' Processing helix chain 'R' and resid 125 through 145 Processing helix chain 'R' and resid 169 through 181 removed outlier: 3.858A pdb=" N LEU R 174 " --> pdb=" O ALA R 170 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA R 175 " --> pdb=" O TRP R 171 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 202 Processing helix chain 'R' and resid 359 through 397 removed outlier: 3.632A pdb=" N THR R 364 " --> pdb=" O ARG R 360 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG R 365 " --> pdb=" O ALA R 361 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS R 367 " --> pdb=" O LEU R 363 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE R 377 " --> pdb=" O LEU R 373 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE R 380 " --> pdb=" O VAL R 376 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL R 381 " --> pdb=" O ILE R 377 " (cutoff:3.500A) Proline residue: R 386 - end of helix removed outlier: 3.877A pdb=" N GLY R 394 " --> pdb=" O SER R 390 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA R 395 " --> pdb=" O TYR R 391 " (cutoff:3.500A) Processing helix chain 'R' and resid 406 through 417 removed outlier: 3.813A pdb=" N PHE R 410 " --> pdb=" O GLY R 406 " (cutoff:3.500A) Processing helix chain 'R' and resid 417 through 429 Proline residue: R 423 - end of helix removed outlier: 3.745A pdb=" N TYR R 426 " --> pdb=" O ASN R 422 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR R 427 " --> pdb=" O PRO R 423 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE R 428 " --> pdb=" O VAL R 424 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE R 429 " --> pdb=" O ILE R 425 " (cutoff:3.500A) Processing helix chain 'R' and resid 430 through 442 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 190 removed outlier: 3.800A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N HIS A 322 " --> pdb=" O LEU A 266 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 268 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 49 through 51 removed outlier: 3.840A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 61 through 62 removed outlier: 3.527A pdb=" N HIS B 62 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.168A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.114A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 190 through 192 removed outlier: 4.099A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.736A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N PHE B 241 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.621A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 128 through 130 removed outlier: 3.642A pdb=" N ARG H 148 " --> pdb=" O THR H 129 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 135 through 136 removed outlier: 6.109A pdb=" N VAL H 135 " --> pdb=" O GLU H 234 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP H 164 " --> pdb=" O LEU H 176 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 191 through 196 339 hydrogen bonds defined for protein. 966 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: 2.17 Time building geometry restraints manager: 2.45 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: 2622 1.34 - 1.46: 1721 1.46 - 1.58: 4582 1.58 - 1.70: 1 1.70 - 1.82: 79 Bond restraints: 9005 Sorted by residual: bond pdb=" C09 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.385 1.529 -0.144 2.00e-02 2.50e+03 5.17e+01 bond pdb=" C11 CZX R 501 " pdb=" C12 CZX R 501 " ideal model delta sigma weight residual 1.386 1.528 -0.142 2.00e-02 2.50e+03 5.07e+01 bond pdb=" C08 CZX R 501 " pdb=" C11 CZX R 501 " ideal model delta sigma weight residual 1.392 1.528 -0.136 2.00e-02 2.50e+03 4.62e+01 bond pdb=" C04 CZX R 501 " pdb=" C09 CZX R 501 " ideal model delta sigma weight residual 1.393 1.526 -0.133 2.00e-02 2.50e+03 4.41e+01 bond pdb=" C04 CZX R 501 " pdb=" C05 CZX R 501 " ideal model delta sigma weight residual 1.403 1.530 -0.127 2.00e-02 2.50e+03 4.01e+01 ... (remaining 9000 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 11801 1.94 - 3.87: 316 3.87 - 5.81: 45 5.81 - 7.75: 20 7.75 - 9.69: 9 Bond angle restraints: 12191 Sorted by residual: angle pdb=" N ILE R 396 " pdb=" CA ILE R 396 " pdb=" C ILE R 396 " ideal model delta sigma weight residual 110.82 101.31 9.51 9.70e-01 1.06e+00 9.61e+01 angle pdb=" C ASN H 157 " pdb=" N GLY H 158 " pdb=" CA GLY H 158 " ideal model delta sigma weight residual 121.70 131.39 -9.69 1.80e+00 3.09e-01 2.90e+01 angle pdb=" C TYR R 79 " pdb=" N PHE R 80 " pdb=" CA PHE R 80 " ideal model delta sigma weight residual 121.54 130.87 -9.33 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C PHE R 80 " pdb=" N ARG R 81 " pdb=" CA ARG R 81 " ideal model delta sigma weight residual 121.54 130.81 -9.27 1.91e+00 2.74e-01 2.35e+01 angle pdb=" CA ALA R 395 " pdb=" C ALA R 395 " pdb=" N ILE R 396 " ideal model delta sigma weight residual 118.81 113.25 5.56 1.15e+00 7.56e-01 2.34e+01 ... (remaining 12186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.97: 5108 14.97 - 29.95: 173 29.95 - 44.92: 56 44.92 - 59.89: 8 59.89 - 74.86: 3 Dihedral angle restraints: 5348 sinusoidal: 2102 harmonic: 3246 Sorted by residual: dihedral pdb=" CA PRO R 146 " pdb=" C PRO R 146 " pdb=" N PRO R 147 " pdb=" CA PRO R 147 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ILE A 19 " pdb=" C ILE A 19 " pdb=" N ASP A 20 " pdb=" CA ASP A 20 " ideal model delta harmonic sigma weight residual 180.00 159.00 21.00 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 59.10 33.90 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 5345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1139 0.061 - 0.123: 198 0.123 - 0.184: 32 0.184 - 0.246: 2 0.246 - 0.307: 2 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ILE R 396 " pdb=" N ILE R 396 " pdb=" C ILE R 396 " pdb=" CB ILE R 396 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" C03 CZX R 501 " pdb=" C04 CZX R 501 " pdb=" C06 CZX R 501 " pdb=" C07 CZX R 501 " both_signs ideal model delta sigma weight residual False -2.47 -2.76 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA CYS R 397 " pdb=" N CYS R 397 " pdb=" C CYS R 397 " pdb=" CB CYS R 397 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 1370 not shown) Planarity restraints: 1537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO R 146 " 0.063 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO R 147 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO R 147 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO R 147 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 340 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.85e+00 pdb=" C THR A 340 " 0.042 2.00e-02 2.50e+03 pdb=" O THR A 340 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 341 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 395 " 0.011 2.00e-02 2.50e+03 2.40e-02 5.78e+00 pdb=" C ALA R 395 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA R 395 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE R 396 " 0.014 2.00e-02 2.50e+03 ... (remaining 1534 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2380 2.81 - 3.33: 7240 3.33 - 3.86: 13758 3.86 - 4.38: 15383 4.38 - 4.90: 27036 Nonbonded interactions: 65797 Sorted by model distance: nonbonded pdb=" OG SER R 69 " pdb=" OH TYR R 88 " model vdw 2.288 3.040 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.302 3.040 nonbonded pdb=" O PRO R 423 " pdb=" OG1 THR R 427 " model vdw 2.323 3.040 nonbonded pdb=" O LEU B 30 " pdb=" OG1 THR B 34 " model vdw 2.343 3.040 nonbonded pdb=" O CYS R 397 " pdb=" N CYS R 401 " model vdw 2.345 3.120 ... (remaining 65792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.320 Find NCS groups from input model: 0.090 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 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 0.144 9005 Z= 0.383 Angle : 0.823 9.687 12191 Z= 0.478 Chirality : 0.049 0.307 1373 Planarity : 0.007 0.094 1537 Dihedral : 9.237 74.864 3241 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.31 % Allowed : 1.78 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.19), residues: 1095 helix: -2.64 (0.19), residues: 340 sheet: -2.22 (0.30), residues: 242 loop : -3.42 (0.21), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.010 0.001 HIS R 102 PHE 0.031 0.002 PHE R 369 TYR 0.017 0.002 TYR R 79 ARG 0.005 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 431 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.7535 (pp) cc_final: 0.7222 (pp) REVERT: A 49 ILE cc_start: 0.6716 (pt) cc_final: 0.6462 (pt) REVERT: A 50 VAL cc_start: 0.6760 (m) cc_final: 0.6501 (m) REVERT: B 43 ILE cc_start: 0.7437 (mm) cc_final: 0.6307 (mm) REVERT: B 280 LYS cc_start: 0.6658 (tptt) cc_final: 0.6209 (tptm) REVERT: B 313 ASN cc_start: 0.7856 (t0) cc_final: 0.7340 (m-40) REVERT: R 102 HIS cc_start: 0.6568 (m-70) cc_final: 0.5985 (m-70) REVERT: R 414 ILE cc_start: 0.7376 (mm) cc_final: 0.7152 (mm) REVERT: R 429 PHE cc_start: 0.6872 (m-10) cc_final: 0.6657 (m-10) REVERT: H 58 ILE cc_start: 0.8045 (mt) cc_final: 0.7839 (mt) outliers start: 1 outliers final: 1 residues processed: 431 average time/residue: 0.2407 time to fit residues: 135.4442 Evaluate side-chains 283 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 282 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 56 optimal weight: 0.0070 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 33 optimal weight: 0.1980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN A 244 HIS A 304 GLN A 346 ASN B 16 ASN B 75 GLN B 239 ASN ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 295 ASN B 311 HIS R 30 ASN R 121 ASN ** R 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 418 ASN H 155 HIS H 159 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6726 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9005 Z= 0.184 Angle : 0.619 7.064 12191 Z= 0.332 Chirality : 0.043 0.275 1373 Planarity : 0.005 0.079 1537 Dihedral : 4.672 23.124 1225 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 0.21 % Allowed : 2.20 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.22), residues: 1095 helix: -0.63 (0.26), residues: 332 sheet: -1.83 (0.30), residues: 249 loop : -2.89 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 84 HIS 0.008 0.001 HIS H 155 PHE 0.031 0.002 PHE R 369 TYR 0.020 0.002 TYR H 216 ARG 0.007 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 MET cc_start: 0.7439 (tpp) cc_final: 0.7142 (ttm) REVERT: A 227 LEU cc_start: 0.7128 (mt) cc_final: 0.6766 (mt) REVERT: A 246 SER cc_start: 0.8693 (m) cc_final: 0.8363 (m) REVERT: B 68 ARG cc_start: 0.7799 (tpt-90) cc_final: 0.6986 (ttt-90) REVERT: B 211 TRP cc_start: 0.7824 (m100) cc_final: 0.7620 (m100) REVERT: B 280 LYS cc_start: 0.6943 (tptt) cc_final: 0.6489 (tptm) REVERT: B 313 ASN cc_start: 0.7696 (t0) cc_final: 0.7365 (m-40) REVERT: R 414 ILE cc_start: 0.7584 (mm) cc_final: 0.7323 (mm) REVERT: R 418 ASN cc_start: 0.5375 (t0) cc_final: 0.4767 (t0) REVERT: H 93 MET cc_start: 0.5919 (tpp) cc_final: 0.5518 (tpp) outliers start: 0 outliers final: 0 residues processed: 327 average time/residue: 0.1934 time to fit residues: 87.2966 Evaluate side-chains 257 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 257 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 3.9990 chunk 31 optimal weight: 0.0870 chunk 83 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 100 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 304 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 293 ASN R 30 ASN R 362 GLN ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.4772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9005 Z= 0.212 Angle : 0.638 9.095 12191 Z= 0.339 Chirality : 0.043 0.241 1373 Planarity : 0.005 0.070 1537 Dihedral : 4.646 23.020 1225 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.42 % Allowed : 2.20 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.24), residues: 1095 helix: 0.23 (0.28), residues: 338 sheet: -1.60 (0.32), residues: 243 loop : -2.60 (0.23), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 111 HIS 0.008 0.002 HIS H 155 PHE 0.031 0.002 PHE R 369 TYR 0.018 0.002 TYR H 216 ARG 0.011 0.001 ARG B 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 344 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8276 (pt) cc_final: 0.8016 (mt) REVERT: A 210 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7915 (mmmt) REVERT: A 227 LEU cc_start: 0.7428 (mt) cc_final: 0.7182 (mt) REVERT: A 339 VAL cc_start: 0.8612 (t) cc_final: 0.8274 (t) REVERT: B 188 MET cc_start: 0.8291 (tpp) cc_final: 0.7742 (mpp) REVERT: B 251 ARG cc_start: 0.7839 (mtt90) cc_final: 0.7209 (mmt90) REVERT: B 261 LEU cc_start: 0.8193 (mt) cc_final: 0.7924 (mt) REVERT: B 280 LYS cc_start: 0.6584 (tptt) cc_final: 0.6378 (tmtt) REVERT: R 32 LEU cc_start: 0.7142 (tt) cc_final: 0.6721 (tp) REVERT: R 49 LEU cc_start: 0.8807 (mm) cc_final: 0.8523 (mm) REVERT: R 414 ILE cc_start: 0.8038 (mm) cc_final: 0.7697 (mm) REVERT: H 39 GLN cc_start: 0.6865 (tp40) cc_final: 0.6452 (tt0) REVERT: H 58 ILE cc_start: 0.8276 (mt) cc_final: 0.8072 (mt) REVERT: H 82 GLN cc_start: 0.6361 (pm20) cc_final: 0.5554 (mp10) REVERT: H 103 TYR cc_start: 0.7177 (t80) cc_final: 0.6794 (t80) outliers start: 2 outliers final: 1 residues processed: 344 average time/residue: 0.2115 time to fit residues: 97.8545 Evaluate side-chains 266 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 265 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 0.0770 chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 0.0020 chunk 28 optimal weight: 1.9990 overall best weight: 0.3346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 204 GLN A 304 GLN B 176 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 266 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN R 30 ASN R 102 HIS ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 362 GLN H 155 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9005 Z= 0.171 Angle : 0.622 7.329 12191 Z= 0.327 Chirality : 0.043 0.237 1373 Planarity : 0.004 0.061 1537 Dihedral : 4.552 21.511 1225 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.31 % Allowed : 1.47 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -1.89 (0.24), residues: 1095 helix: 0.48 (0.28), residues: 334 sheet: -1.47 (0.33), residues: 242 loop : -2.35 (0.24), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 111 HIS 0.018 0.002 HIS R 102 PHE 0.032 0.002 PHE R 181 TYR 0.014 0.002 TYR B 59 ARG 0.005 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 320 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8385 (pt) cc_final: 0.8162 (mt) REVERT: A 210 LYS cc_start: 0.8492 (mmtt) cc_final: 0.7968 (mmmt) REVERT: A 227 LEU cc_start: 0.7851 (mt) cc_final: 0.7571 (mt) REVERT: A 252 SER cc_start: 0.8764 (p) cc_final: 0.8529 (p) REVERT: A 346 ASN cc_start: 0.8533 (m110) cc_final: 0.8316 (m-40) REVERT: B 188 MET cc_start: 0.8460 (tpp) cc_final: 0.7952 (mpp) REVERT: B 251 ARG cc_start: 0.7917 (mtt90) cc_final: 0.6741 (mtt180) REVERT: R 107 SER cc_start: 0.8466 (t) cc_final: 0.8230 (t) REVERT: R 370 THR cc_start: 0.7154 (p) cc_final: 0.6909 (t) REVERT: R 414 ILE cc_start: 0.7763 (mm) cc_final: 0.7524 (mm) REVERT: R 427 THR cc_start: 0.8668 (p) cc_final: 0.8419 (p) REVERT: H 82 GLN cc_start: 0.6448 (pm20) cc_final: 0.5668 (mp10) REVERT: H 103 TYR cc_start: 0.7266 (t80) cc_final: 0.6930 (t80) REVERT: H 225 LEU cc_start: 0.8587 (mt) cc_final: 0.8336 (mm) outliers start: 1 outliers final: 0 residues processed: 321 average time/residue: 0.2040 time to fit residues: 88.7765 Evaluate side-chains 259 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0670 chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 73 optimal weight: 0.0070 chunk 0 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 95 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 16 ASN B 156 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS G 11 GLN R 30 ASN ** R 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 155 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.6065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9005 Z= 0.211 Angle : 0.646 9.018 12191 Z= 0.337 Chirality : 0.044 0.292 1373 Planarity : 0.005 0.062 1537 Dihedral : 4.630 19.580 1225 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.21 % Allowed : 1.78 % Favored : 98.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -1.74 (0.25), residues: 1095 helix: 0.67 (0.28), residues: 335 sheet: -1.35 (0.33), residues: 250 loop : -2.34 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 111 HIS 0.004 0.001 HIS B 54 PHE 0.024 0.002 PHE R 369 TYR 0.013 0.002 TYR B 59 ARG 0.005 0.001 ARG H 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 328 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8649 (pt) cc_final: 0.8385 (mt) REVERT: A 210 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8228 (mmmt) REVERT: A 346 ASN cc_start: 0.8385 (m110) cc_final: 0.8123 (m110) REVERT: B 30 LEU cc_start: 0.6541 (mt) cc_final: 0.6006 (mt) REVERT: B 86 THR cc_start: 0.8035 (p) cc_final: 0.7589 (p) REVERT: B 88 ASN cc_start: 0.8786 (m-40) cc_final: 0.8226 (m-40) REVERT: B 173 THR cc_start: 0.6964 (p) cc_final: 0.6709 (p) REVERT: B 175 GLN cc_start: 0.8206 (pm20) cc_final: 0.7830 (pm20) REVERT: B 246 ASP cc_start: 0.7014 (m-30) cc_final: 0.6777 (m-30) REVERT: B 251 ARG cc_start: 0.8192 (mtt90) cc_final: 0.7754 (mtt-85) REVERT: R 44 ARG cc_start: 0.8365 (mtt180) cc_final: 0.7588 (mtt-85) REVERT: R 98 SER cc_start: 0.8819 (p) cc_final: 0.8120 (p) REVERT: R 102 HIS cc_start: 0.7680 (m170) cc_final: 0.7188 (m170) REVERT: R 107 SER cc_start: 0.8372 (t) cc_final: 0.8096 (t) REVERT: R 370 THR cc_start: 0.7253 (p) cc_final: 0.6994 (t) REVERT: R 414 ILE cc_start: 0.7749 (mm) cc_final: 0.7502 (mm) REVERT: R 422 ASN cc_start: 0.6074 (m110) cc_final: 0.5828 (m-40) REVERT: R 427 THR cc_start: 0.8711 (p) cc_final: 0.8507 (p) REVERT: H 34 MET cc_start: 0.8524 (mmt) cc_final: 0.8298 (mmt) REVERT: H 57 THR cc_start: 0.8016 (m) cc_final: 0.7661 (m) REVERT: H 82 GLN cc_start: 0.6423 (pm20) cc_final: 0.5582 (mp10) REVERT: H 103 TYR cc_start: 0.7580 (t80) cc_final: 0.7374 (t80) REVERT: H 206 ARG cc_start: 0.7662 (ptt180) cc_final: 0.7220 (mmp80) REVERT: H 225 LEU cc_start: 0.8830 (mt) cc_final: 0.8419 (mm) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2096 time to fit residues: 92.3405 Evaluate side-chains 268 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 102 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN R 30 ASN R 422 ASN H 155 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.6730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9005 Z= 0.243 Angle : 0.667 7.527 12191 Z= 0.351 Chirality : 0.045 0.280 1373 Planarity : 0.004 0.065 1537 Dihedral : 4.796 18.246 1225 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.21 % Allowed : 1.57 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -1.74 (0.24), residues: 1095 helix: 0.55 (0.28), residues: 340 sheet: -1.25 (0.32), residues: 256 loop : -2.35 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 111 HIS 0.006 0.001 HIS A 244 PHE 0.024 0.002 PHE R 369 TYR 0.015 0.002 TYR R 416 ARG 0.007 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8636 (pt) cc_final: 0.8297 (mt) REVERT: A 210 LYS cc_start: 0.8466 (mmtt) cc_final: 0.8119 (mmmt) REVERT: A 346 ASN cc_start: 0.8267 (m110) cc_final: 0.8018 (m-40) REVERT: B 86 THR cc_start: 0.8489 (p) cc_final: 0.7991 (p) REVERT: B 88 ASN cc_start: 0.8829 (m-40) cc_final: 0.8278 (m-40) REVERT: B 175 GLN cc_start: 0.8185 (pm20) cc_final: 0.7870 (pm20) REVERT: B 251 ARG cc_start: 0.8144 (mtt90) cc_final: 0.7917 (mtt-85) REVERT: R 83 THR cc_start: 0.7458 (p) cc_final: 0.7182 (p) REVERT: R 88 TYR cc_start: 0.6530 (t80) cc_final: 0.6316 (t80) REVERT: R 370 THR cc_start: 0.7426 (p) cc_final: 0.7177 (t) REVERT: R 373 LEU cc_start: 0.8271 (mt) cc_final: 0.8070 (mt) REVERT: R 377 ILE cc_start: 0.8279 (tp) cc_final: 0.8001 (tp) REVERT: R 414 ILE cc_start: 0.7811 (mm) cc_final: 0.7532 (mm) REVERT: R 422 ASN cc_start: 0.6339 (m-40) cc_final: 0.5860 (m110) REVERT: H 189 ASP cc_start: 0.7637 (t0) cc_final: 0.7410 (t0) REVERT: H 206 ARG cc_start: 0.7663 (ptt180) cc_final: 0.7252 (mmp-170) REVERT: H 225 LEU cc_start: 0.8831 (mt) cc_final: 0.8267 (mt) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2197 time to fit residues: 93.9345 Evaluate side-chains 260 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 260 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.4980 chunk 66 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 16 ASN ** B 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 GLN R 30 ASN H 39 GLN H 155 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.7112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9005 Z= 0.231 Angle : 0.675 7.386 12191 Z= 0.356 Chirality : 0.047 0.283 1373 Planarity : 0.004 0.062 1537 Dihedral : 4.819 18.879 1225 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.21 % Allowed : 2.51 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -1.65 (0.24), residues: 1095 helix: 0.70 (0.28), residues: 335 sheet: -1.19 (0.32), residues: 247 loop : -2.32 (0.25), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 111 HIS 0.006 0.001 HIS B 54 PHE 0.022 0.002 PHE B 241 TYR 0.011 0.002 TYR R 416 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 312 time to evaluate : 1.053 Fit side-chains revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8795 (pt) cc_final: 0.8476 (mt) REVERT: A 210 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8206 (mmmt) REVERT: B 86 THR cc_start: 0.8593 (p) cc_final: 0.7972 (p) REVERT: B 88 ASN cc_start: 0.8872 (m-40) cc_final: 0.8353 (m-40) REVERT: B 175 GLN cc_start: 0.8308 (pm20) cc_final: 0.8062 (pm20) REVERT: G 38 MET cc_start: 0.4862 (ptm) cc_final: 0.4657 (ptm) REVERT: R 44 ARG cc_start: 0.8376 (mtt180) cc_final: 0.8152 (mtt180) REVERT: R 88 TYR cc_start: 0.6627 (t80) cc_final: 0.6311 (t80) REVERT: R 98 SER cc_start: 0.8759 (p) cc_final: 0.7805 (p) REVERT: R 102 HIS cc_start: 0.7787 (m170) cc_final: 0.7188 (m90) REVERT: R 377 ILE cc_start: 0.8422 (tp) cc_final: 0.8110 (tp) REVERT: R 414 ILE cc_start: 0.7866 (mm) cc_final: 0.7528 (mm) REVERT: R 422 ASN cc_start: 0.6704 (m-40) cc_final: 0.6493 (m-40) REVERT: H 95 TYR cc_start: 0.7292 (m-10) cc_final: 0.7020 (m-10) REVERT: H 138 THR cc_start: 0.6914 (t) cc_final: 0.6441 (m) REVERT: H 225 LEU cc_start: 0.8737 (mt) cc_final: 0.8148 (mt) REVERT: H 226 THR cc_start: 0.8827 (p) cc_final: 0.8615 (p) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.2254 time to fit residues: 94.0506 Evaluate side-chains 261 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.0970 chunk 31 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 92 optimal weight: 0.4980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 GLN B 16 ASN G 11 GLN R 30 ASN H 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.7403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9005 Z= 0.223 Angle : 0.689 10.816 12191 Z= 0.359 Chirality : 0.046 0.267 1373 Planarity : 0.004 0.062 1537 Dihedral : 4.849 18.747 1225 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 0.21 % Allowed : 0.94 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -1.67 (0.24), residues: 1095 helix: 0.62 (0.28), residues: 338 sheet: -1.12 (0.33), residues: 235 loop : -2.32 (0.24), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 111 HIS 0.006 0.001 HIS B 54 PHE 0.034 0.002 PHE R 369 TYR 0.016 0.002 TYR H 215 ARG 0.006 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 319 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 ILE cc_start: 0.8801 (pt) cc_final: 0.8463 (mt) REVERT: A 210 LYS cc_start: 0.8497 (mmtt) cc_final: 0.8110 (mmmt) REVERT: B 75 GLN cc_start: 0.7520 (mm-40) cc_final: 0.7290 (mm-40) REVERT: B 86 THR cc_start: 0.8675 (p) cc_final: 0.8090 (p) REVERT: B 88 ASN cc_start: 0.8958 (m-40) cc_final: 0.8376 (m-40) REVERT: B 188 MET cc_start: 0.8795 (tpp) cc_final: 0.8375 (mmm) REVERT: G 38 MET cc_start: 0.4766 (ptm) cc_final: 0.4548 (ptm) REVERT: G 50 LEU cc_start: 0.7407 (tp) cc_final: 0.7148 (tp) REVERT: R 88 TYR cc_start: 0.6658 (t80) cc_final: 0.6381 (t80) REVERT: R 98 SER cc_start: 0.8788 (p) cc_final: 0.7899 (p) REVERT: R 102 HIS cc_start: 0.7834 (m170) cc_final: 0.7295 (m90) REVERT: R 377 ILE cc_start: 0.8370 (tp) cc_final: 0.8143 (tp) REVERT: R 414 ILE cc_start: 0.8174 (mm) cc_final: 0.7889 (mm) REVERT: H 95 TYR cc_start: 0.7462 (m-10) cc_final: 0.7253 (m-10) REVERT: H 138 THR cc_start: 0.7480 (t) cc_final: 0.6967 (m) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.2135 time to fit residues: 91.4956 Evaluate side-chains 265 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.3980 chunk 101 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 0.6980 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.3980 chunk 64 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN B 220 GLN G 11 GLN R 30 ASN ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9005 Z= 0.215 Angle : 0.699 11.023 12191 Z= 0.363 Chirality : 0.045 0.269 1373 Planarity : 0.004 0.061 1537 Dihedral : 4.829 18.322 1225 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.21 % Allowed : 0.52 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -1.72 (0.24), residues: 1095 helix: 0.50 (0.28), residues: 343 sheet: -1.04 (0.34), residues: 231 loop : -2.38 (0.24), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 84 HIS 0.005 0.001 HIS B 54 PHE 0.037 0.002 PHE R 369 TYR 0.011 0.002 TYR B 289 ARG 0.007 0.001 ARG A 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 210 LYS cc_start: 0.8416 (mmtt) cc_final: 0.8165 (mmmt) REVERT: A 252 SER cc_start: 0.8954 (p) cc_final: 0.8739 (p) REVERT: B 30 LEU cc_start: 0.6512 (tt) cc_final: 0.6018 (tt) REVERT: B 86 THR cc_start: 0.8736 (p) cc_final: 0.8169 (p) REVERT: B 88 ASN cc_start: 0.8984 (m-40) cc_final: 0.8412 (m-40) REVERT: B 156 GLN cc_start: 0.7300 (mm110) cc_final: 0.7090 (mm-40) REVERT: G 50 LEU cc_start: 0.7464 (tp) cc_final: 0.7212 (tp) REVERT: R 98 SER cc_start: 0.8773 (p) cc_final: 0.7884 (p) REVERT: R 102 HIS cc_start: 0.7779 (m170) cc_final: 0.7237 (m90) REVERT: R 377 ILE cc_start: 0.8450 (tp) cc_final: 0.8118 (tp) REVERT: R 414 ILE cc_start: 0.8143 (mm) cc_final: 0.7899 (mm) REVERT: H 82 GLN cc_start: 0.6998 (pm20) cc_final: 0.6606 (pm20) REVERT: H 93 MET cc_start: 0.6711 (tpp) cc_final: 0.4871 (ttt) REVERT: H 95 TYR cc_start: 0.7541 (m-10) cc_final: 0.6909 (m-10) REVERT: H 138 THR cc_start: 0.7431 (t) cc_final: 0.6881 (m) outliers start: 0 outliers final: 0 residues processed: 317 average time/residue: 0.2210 time to fit residues: 93.9693 Evaluate side-chains 274 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 274 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 3.9990 chunk 72 optimal weight: 0.0970 chunk 109 optimal weight: 0.0370 chunk 100 optimal weight: 0.9980 chunk 87 optimal weight: 0.0570 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS G 11 GLN R 30 ASN ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.7835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9005 Z= 0.198 Angle : 0.688 7.862 12191 Z= 0.359 Chirality : 0.045 0.257 1373 Planarity : 0.004 0.061 1537 Dihedral : 4.757 17.654 1225 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 0.21 % Allowed : 0.63 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -1.51 (0.24), residues: 1095 helix: 0.66 (0.28), residues: 342 sheet: -0.88 (0.34), residues: 236 loop : -2.25 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP H 111 HIS 0.006 0.001 HIS B 54 PHE 0.037 0.002 PHE R 369 TYR 0.033 0.002 TYR R 120 ARG 0.005 0.000 ARG B 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8421 (tpm170) cc_final: 0.7717 (tpm170) REVERT: A 210 LYS cc_start: 0.8492 (mmtt) cc_final: 0.8140 (mmmt) REVERT: B 188 MET cc_start: 0.8765 (tpp) cc_final: 0.8418 (mmm) REVERT: G 50 LEU cc_start: 0.7426 (tp) cc_final: 0.7109 (tp) REVERT: R 98 SER cc_start: 0.8744 (p) cc_final: 0.7884 (p) REVERT: R 102 HIS cc_start: 0.7742 (m170) cc_final: 0.7238 (m90) REVERT: R 119 GLU cc_start: 0.7072 (pt0) cc_final: 0.6813 (mt-10) REVERT: R 377 ILE cc_start: 0.8433 (tp) cc_final: 0.8057 (tp) REVERT: R 414 ILE cc_start: 0.7916 (mm) cc_final: 0.7486 (mm) REVERT: H 34 MET cc_start: 0.8149 (mmt) cc_final: 0.7931 (mmt) REVERT: H 82 GLN cc_start: 0.6751 (pm20) cc_final: 0.6475 (pm20) REVERT: H 93 MET cc_start: 0.6781 (tpp) cc_final: 0.4877 (ttt) REVERT: H 95 TYR cc_start: 0.7531 (m-10) cc_final: 0.6929 (m-10) REVERT: H 115 THR cc_start: 0.8273 (p) cc_final: 0.7999 (p) REVERT: H 138 THR cc_start: 0.7389 (t) cc_final: 0.6854 (m) outliers start: 0 outliers final: 0 residues processed: 313 average time/residue: 0.2307 time to fit residues: 95.9386 Evaluate side-chains 267 residues out of total 954 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 4 optimal weight: 0.2980 chunk 63 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 GLN G 11 GLN R 30 ASN ** R 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** H 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.161482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.142744 restraints weight = 30586.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.146904 restraints weight = 35283.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.148485 restraints weight = 14170.402| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 17 | |-----------------------------------------------------------------------------| r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.8009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9005 Z= 0.212 Angle : 0.683 7.302 12191 Z= 0.359 Chirality : 0.045 0.256 1373 Planarity : 0.004 0.061 1537 Dihedral : 4.759 17.869 1225 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.21 % Allowed : 0.31 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.19 % 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: -1.43 (0.25), residues: 1095 helix: 0.68 (0.28), residues: 342 sheet: -0.92 (0.34), residues: 238 loop : -2.14 (0.25), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP H 111 HIS 0.012 0.002 HIS H 155 PHE 0.038 0.002 PHE R 369 TYR 0.040 0.002 TYR R 120 ARG 0.005 0.001 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2483.82 seconds wall clock time: 44 minutes 58.04 seconds (2698.04 seconds total)