Starting phenix.real_space_refine on Mon Mar 11 11:51:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i95_35257/03_2024/8i95_35257.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i95_35257/03_2024/8i95_35257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i95_35257/03_2024/8i95_35257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i95_35257/03_2024/8i95_35257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i95_35257/03_2024/8i95_35257.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i95_35257/03_2024/8i95_35257.pdb" } resolution = 2.88 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= 0.032 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 52 5.16 5 C 5205 2.51 5 N 1403 2.21 5 O 1493 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 8153 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1550 Classifications: {'peptide': 208} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 4, 'TRANS': 203} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 57 Chain: "B" Number of atoms: 2416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2416 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 230 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 103 Chain: "G" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 400 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "H" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1658 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 53 Chain: "C" Number of atoms: 2057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2057 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 41} Link IDs: {'PTRANS': 14, 'TRANS': 265} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 82 Chain: "D" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Classifications: {'peptide': 9} Modifications used: {'COO': 1, 'PEPT-D': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.68, per 1000 atoms: 0.57 Number of scatterers: 8153 At special positions: 0 Unit cell: (85.56, 119.6, 123.28, 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 52 16.00 O 1493 8.00 N 1403 7.00 C 5205 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " distance=2.05 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS C 172 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DAL D 9 " Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 14 sheets defined 37.6% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 8 through 32 removed outlier: 3.796A pdb=" N LYS A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 51 Processing helix chain 'A' and resid 208 through 217 removed outlier: 3.560A pdb=" N LYS A 211 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 257 through 261 removed outlier: 4.130A pdb=" N ILE A 261 " --> pdb=" O LYS A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.549A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'H' and resid 220 through 224 removed outlier: 3.757A pdb=" N VAL H 224 " --> pdb=" O ALA H 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 50 removed outlier: 3.555A pdb=" N SER C 26 " --> pdb=" O PRO C 22 " (cutoff:3.500A) Proline residue: C 39 - end of helix removed outlier: 3.576A pdb=" N VAL C 44 " --> pdb=" O GLY C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 74 removed outlier: 4.104A pdb=" N TRP C 60 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE C 61 " --> pdb=" O ASN C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 84 removed outlier: 3.824A pdb=" N SER C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 126 Proline residue: C 99 - end of helix removed outlier: 5.197A pdb=" N VAL C 103 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL C 110 " --> pdb=" O MET C 106 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.562A pdb=" N ASN C 132 " --> pdb=" O ILE C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 154 Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.766A pdb=" N TYR C 160 " --> pdb=" O PRO C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 363 removed outlier: 5.256A pdb=" N LEU C 347 " --> pdb=" O VAL C 343 " (cutoff:3.500A) Proline residue: C 348 - end of helix Processing helix chain 'C' and resid 373 through 403 Proline residue: C 392 - end of helix removed outlier: 3.953A pdb=" N LEU C 401 " --> pdb=" O GLY C 397 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LEU C 402 " --> pdb=" O VAL C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 407 through 431 removed outlier: 6.367A pdb=" N LEU C 413 " --> pdb=" O LEU C 409 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N HIS C 418 " --> pdb=" O MET C 414 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL C 419 " --> pdb=" O SER C 415 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N SER C 428 " --> pdb=" O ALA C 424 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N CYS C 429 " --> pdb=" O SER C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 435 through 438 removed outlier: 3.820A pdb=" N LEU C 438 " --> pdb=" O TYR C 435 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 435 through 438' Processing helix chain 'C' and resid 439 through 451 removed outlier: 3.827A pdb=" N GLN C 451 " --> pdb=" O ARG C 447 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 191 removed outlier: 6.164A pdb=" N VAL A 34 " --> pdb=" O ARG A 198 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N PHE A 200 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N LEU A 36 " --> pdb=" O PHE A 200 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.813A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.923A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.546A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.569A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.727A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.514A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.648A pdb=" N ARG H 18 " --> pdb=" O MET H 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.527A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 58 through 60 removed outlier: 6.527A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TYR H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'H' and resid 146 through 149 removed outlier: 3.623A pdb=" N VAL H 149 " --> pdb=" O GLU H 246 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU H 178 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU H 187 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 162 through 166 removed outlier: 3.969A pdb=" N PHE C 164 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG C 171 " --> pdb=" O PHE C 164 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1236 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: 2.37 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1623 1.33 - 1.45: 2171 1.45 - 1.58: 4468 1.58 - 1.70: 1 1.70 - 1.83: 67 Bond restraints: 8330 Sorted by residual: bond pdb=" CA THR C 331 " pdb=" CB THR C 331 " ideal model delta sigma weight residual 1.540 1.642 -0.102 2.70e-02 1.37e+03 1.44e+01 bond pdb=" C PRO C 156 " pdb=" O PRO C 156 " ideal model delta sigma weight residual 1.237 1.203 0.034 1.32e-02 5.74e+03 6.79e+00 bond pdb=" N ILE C 155 " pdb=" CA ILE C 155 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.23e-02 6.61e+03 6.67e+00 bond pdb=" CA THR C 331 " pdb=" C THR C 331 " ideal model delta sigma weight residual 1.525 1.576 -0.051 2.10e-02 2.27e+03 5.96e+00 bond pdb=" N PRO C 156 " pdb=" CA PRO C 156 " ideal model delta sigma weight residual 1.471 1.443 0.028 1.32e-02 5.74e+03 4.49e+00 ... (remaining 8325 not shown) Histogram of bond angle deviations from ideal: 97.13 - 104.51: 108 104.51 - 111.89: 4150 111.89 - 119.27: 2632 119.27 - 126.65: 4338 126.65 - 134.03: 131 Bond angle restraints: 11359 Sorted by residual: angle pdb=" CA THR C 331 " pdb=" C THR C 331 " pdb=" N PRO C 332 " ideal model delta sigma weight residual 116.90 124.88 -7.98 1.50e+00 4.44e-01 2.83e+01 angle pdb=" C PRO C 156 " pdb=" N VAL C 157 " pdb=" CA VAL C 157 " ideal model delta sigma weight residual 121.77 114.35 7.42 1.44e+00 4.82e-01 2.65e+01 angle pdb=" C CYS C 154 " pdb=" N ILE C 155 " pdb=" CA ILE C 155 " ideal model delta sigma weight residual 122.13 115.07 7.06 1.85e+00 2.92e-01 1.46e+01 angle pdb=" N PRO C 156 " pdb=" CA PRO C 156 " pdb=" C PRO C 156 " ideal model delta sigma weight residual 113.84 109.29 4.55 1.30e+00 5.92e-01 1.22e+01 angle pdb=" C ARG D 10 " pdb=" CA ARG D 10 " pdb=" CB ARG D 10 " ideal model delta sigma weight residual 110.10 116.53 -6.43 1.90e+00 2.77e-01 1.15e+01 ... (remaining 11354 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4377 17.53 - 35.05: 380 35.05 - 52.58: 75 52.58 - 70.11: 8 70.11 - 87.63: 8 Dihedral angle restraints: 4848 sinusoidal: 1617 harmonic: 3231 Sorted by residual: dihedral pdb=" CB CYS H 159 " pdb=" SG CYS H 159 " pdb=" SG CYS H 229 " pdb=" CB CYS H 229 " ideal model delta sinusoidal sigma weight residual 93.00 37.84 55.16 1 1.00e+01 1.00e-02 4.12e+01 dihedral pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " pdb=" SG CYS C 172 " pdb=" CB CYS C 172 " ideal model delta sinusoidal sigma weight residual -86.00 -121.90 35.90 1 1.00e+01 1.00e-02 1.82e+01 dihedral pdb=" CA PRO C 99 " pdb=" C PRO C 99 " pdb=" N SER C 100 " pdb=" CA SER C 100 " ideal model delta harmonic sigma weight residual 180.00 161.15 18.85 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1079 0.052 - 0.104: 206 0.104 - 0.156: 42 0.156 - 0.207: 1 0.207 - 0.259: 1 Chirality restraints: 1329 Sorted by residual: chirality pdb=" CA DAL D 9 " pdb=" N DAL D 9 " pdb=" C DAL D 9 " pdb=" CB DAL D 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.23 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA THR C 391 " pdb=" N THR C 391 " pdb=" C THR C 391 " pdb=" CB THR C 391 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CB ILE C 155 " pdb=" CA ILE C 155 " pdb=" CG1 ILE C 155 " pdb=" CG2 ILE C 155 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1326 not shown) Planarity restraints: 1449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 21 " -0.063 5.00e-02 4.00e+02 9.39e-02 1.41e+01 pdb=" N PRO C 22 " 0.162 5.00e-02 4.00e+02 pdb=" CA PRO C 22 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 22 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 347 " -0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO C 348 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO C 348 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 348 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 258 " -0.010 2.00e-02 2.50e+03 1.89e-02 3.58e+00 pdb=" C ASP B 258 " 0.033 2.00e-02 2.50e+03 pdb=" O ASP B 258 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN B 259 " -0.011 2.00e-02 2.50e+03 ... (remaining 1446 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 565 2.74 - 3.28: 8023 3.28 - 3.82: 13786 3.82 - 4.36: 16328 4.36 - 4.90: 29141 Nonbonded interactions: 67843 Sorted by model distance: nonbonded pdb=" O LEU C 387 " pdb=" OG1 THR C 391 " model vdw 2.195 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.211 2.440 nonbonded pdb=" NZ LYS C 96 " pdb=" O ARG C 161 " model vdw 2.241 2.520 nonbonded pdb=" OG1 THR B 321 " pdb=" OD1 ASP B 323 " model vdw 2.268 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.272 2.440 ... (remaining 67838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.630 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: 12.740 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.700 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 8330 Z= 0.229 Angle : 0.608 8.462 11359 Z= 0.323 Chirality : 0.043 0.259 1329 Planarity : 0.005 0.094 1449 Dihedral : 14.093 87.632 2753 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.15 % Allowed : 14.01 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1098 helix: 1.29 (0.28), residues: 380 sheet: -0.22 (0.29), residues: 304 loop : -0.77 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE C 107 TYR 0.021 0.002 TYR B 105 ARG 0.008 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 103 time to evaluate : 0.888 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 108 average time/residue: 0.9682 time to fit residues: 112.7372 Evaluate side-chains 108 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 100 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain D residue 10 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 0.0170 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.0706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8330 Z= 0.228 Angle : 0.547 7.563 11359 Z= 0.290 Chirality : 0.043 0.216 1329 Planarity : 0.004 0.061 1449 Dihedral : 5.149 44.346 1205 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.17 % Allowed : 14.27 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.26), residues: 1098 helix: 1.42 (0.28), residues: 387 sheet: -0.22 (0.29), residues: 287 loop : -0.67 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 339 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE C 107 TYR 0.017 0.001 TYR H 190 ARG 0.003 0.000 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 105 time to evaluate : 0.904 Fit side-chains REVERT: A 254 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.7850 (tp) REVERT: H 140 MET cc_start: 0.8516 (mtp) cc_final: 0.8214 (mtp) REVERT: H 213 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8276 (t) REVERT: C 367 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.7190 (ttt-90) outliers start: 17 outliers final: 10 residues processed: 115 average time/residue: 0.9274 time to fit residues: 115.2728 Evaluate side-chains 111 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 331 THR Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 107 optimal weight: 0.4980 chunk 88 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 79 optimal weight: 0.7980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8330 Z= 0.219 Angle : 0.528 7.414 11359 Z= 0.278 Chirality : 0.042 0.198 1329 Planarity : 0.004 0.054 1449 Dihedral : 4.494 34.998 1194 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 3.31 % Allowed : 15.67 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1098 helix: 1.52 (0.28), residues: 384 sheet: -0.30 (0.29), residues: 287 loop : -0.66 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS H 232 PHE 0.011 0.001 PHE C 107 TYR 0.015 0.001 TYR H 190 ARG 0.002 0.000 ARG D 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 0.937 Fit side-chains REVERT: A 254 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.7904 (tp) REVERT: B 325 MET cc_start: 0.8823 (tpp) cc_final: 0.8321 (mmt) REVERT: H 82 GLN cc_start: 0.8232 (tp40) cc_final: 0.7401 (tp40) REVERT: H 213 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8382 (t) REVERT: C 367 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7183 (ttt-90) outliers start: 26 outliers final: 11 residues processed: 120 average time/residue: 0.9409 time to fit residues: 122.3341 Evaluate side-chains 119 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 47 optimal weight: 0.0270 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 chunk 94 optimal weight: 0.9990 chunk 28 optimal weight: 0.4980 chunk 87 optimal weight: 2.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8330 Z= 0.221 Angle : 0.525 7.614 11359 Z= 0.274 Chirality : 0.042 0.196 1329 Planarity : 0.004 0.053 1449 Dihedral : 4.295 24.809 1191 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.31 % Allowed : 16.82 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1098 helix: 1.57 (0.28), residues: 384 sheet: -0.36 (0.29), residues: 287 loop : -0.66 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS G 44 PHE 0.011 0.001 PHE C 107 TYR 0.015 0.001 TYR B 59 ARG 0.002 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 104 time to evaluate : 0.915 Fit side-chains REVERT: A 254 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.7945 (tp) REVERT: H 213 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8391 (t) REVERT: C 367 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7240 (ttt-90) outliers start: 26 outliers final: 14 residues processed: 122 average time/residue: 0.9314 time to fit residues: 122.9314 Evaluate side-chains 121 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Chi-restraints excluded: chain D residue 4 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.0370 chunk 1 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.0970 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8330 Z= 0.209 Angle : 0.526 7.743 11359 Z= 0.271 Chirality : 0.042 0.193 1329 Planarity : 0.004 0.051 1449 Dihedral : 4.260 24.883 1191 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.31 % Allowed : 17.32 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.26), residues: 1098 helix: 1.64 (0.28), residues: 384 sheet: -0.41 (0.29), residues: 286 loop : -0.65 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 PHE 0.011 0.001 PHE C 107 TYR 0.015 0.001 TYR B 59 ARG 0.002 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 108 time to evaluate : 0.940 Fit side-chains REVERT: A 254 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7966 (tp) REVERT: B 46 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7265 (mmm160) REVERT: H 213 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8398 (t) REVERT: C 367 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7221 (ttt-90) outliers start: 26 outliers final: 13 residues processed: 124 average time/residue: 0.9165 time to fit residues: 123.1524 Evaluate side-chains 119 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 26 optimal weight: 0.4980 chunk 105 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8330 Z= 0.296 Angle : 0.570 8.999 11359 Z= 0.291 Chirality : 0.044 0.201 1329 Planarity : 0.004 0.051 1449 Dihedral : 4.417 26.961 1191 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.44 % Allowed : 17.96 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1098 helix: 1.55 (0.28), residues: 383 sheet: -0.49 (0.29), residues: 287 loop : -0.76 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE C 107 TYR 0.021 0.002 TYR B 59 ARG 0.003 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 0.958 Fit side-chains REVERT: A 254 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7950 (tp) REVERT: B 46 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7267 (mmm160) REVERT: B 160 SER cc_start: 0.9113 (OUTLIER) cc_final: 0.8893 (p) REVERT: H 213 THR cc_start: 0.8647 (OUTLIER) cc_final: 0.8396 (t) REVERT: C 367 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7189 (ttt-90) outliers start: 27 outliers final: 16 residues processed: 126 average time/residue: 0.9043 time to fit residues: 123.3323 Evaluate side-chains 129 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain A residue 261 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 113 GLN Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 341 LEU Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.1980 chunk 60 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 64 optimal weight: 0.6980 chunk 48 optimal weight: 0.3980 chunk 41 optimal weight: 0.2980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8330 Z= 0.191 Angle : 0.529 8.827 11359 Z= 0.270 Chirality : 0.042 0.189 1329 Planarity : 0.004 0.049 1449 Dihedral : 4.265 25.117 1191 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 3.69 % Allowed : 18.09 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1098 helix: 1.63 (0.28), residues: 386 sheet: -0.47 (0.29), residues: 286 loop : -0.65 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 PHE 0.010 0.001 PHE C 107 TYR 0.019 0.001 TYR B 59 ARG 0.001 0.000 ARG C 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 0.833 Fit side-chains REVERT: A 254 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7982 (tp) REVERT: B 13 GLN cc_start: 0.7680 (tt0) cc_final: 0.7116 (tm-30) REVERT: B 46 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7290 (mmm160) REVERT: B 139 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8122 (mt) REVERT: B 160 SER cc_start: 0.8977 (OUTLIER) cc_final: 0.8769 (p) REVERT: H 213 THR cc_start: 0.8649 (OUTLIER) cc_final: 0.8396 (t) REVERT: C 367 ARG cc_start: 0.7527 (OUTLIER) cc_final: 0.7205 (ttt-90) outliers start: 29 outliers final: 15 residues processed: 125 average time/residue: 0.9003 time to fit residues: 121.9842 Evaluate side-chains 123 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 340 ARG Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8330 Z= 0.290 Angle : 0.571 9.984 11359 Z= 0.291 Chirality : 0.044 0.195 1329 Planarity : 0.004 0.051 1449 Dihedral : 4.466 27.446 1191 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.44 % Allowed : 18.73 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.26), residues: 1098 helix: 1.54 (0.28), residues: 385 sheet: -0.52 (0.29), residues: 287 loop : -0.73 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS H 35 PHE 0.012 0.001 PHE C 107 TYR 0.021 0.002 TYR B 59 ARG 0.003 0.000 ARG H 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 104 time to evaluate : 0.910 Fit side-chains REVERT: A 254 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.7955 (tp) REVERT: B 13 GLN cc_start: 0.7582 (tt0) cc_final: 0.7022 (tm-30) REVERT: B 46 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7274 (mmm160) REVERT: B 160 SER cc_start: 0.9115 (OUTLIER) cc_final: 0.8888 (p) REVERT: H 213 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8383 (t) REVERT: C 163 ILE cc_start: 0.7501 (mt) cc_final: 0.7028 (tp) REVERT: C 367 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7152 (ttt-90) outliers start: 27 outliers final: 15 residues processed: 122 average time/residue: 0.9060 time to fit residues: 119.7952 Evaluate side-chains 123 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 76 optimal weight: 0.0070 chunk 30 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 92 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8330 Z= 0.239 Angle : 0.553 9.383 11359 Z= 0.282 Chirality : 0.043 0.192 1329 Planarity : 0.004 0.050 1449 Dihedral : 4.401 26.580 1191 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 3.31 % Allowed : 18.98 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.26), residues: 1098 helix: 1.60 (0.28), residues: 384 sheet: -0.51 (0.29), residues: 286 loop : -0.71 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.002 0.001 HIS B 311 PHE 0.011 0.001 PHE C 107 TYR 0.019 0.001 TYR B 59 ARG 0.003 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 105 time to evaluate : 0.953 Fit side-chains REVERT: A 254 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7987 (tp) REVERT: B 13 GLN cc_start: 0.7550 (tt0) cc_final: 0.7329 (tt0) REVERT: B 46 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7285 (mmm160) REVERT: B 259 GLN cc_start: 0.8651 (OUTLIER) cc_final: 0.8426 (pm20) REVERT: B 325 MET cc_start: 0.8831 (tpp) cc_final: 0.8351 (mmt) REVERT: H 82 GLN cc_start: 0.8304 (tp40) cc_final: 0.7954 (tp40) REVERT: H 213 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8390 (t) REVERT: C 36 LEU cc_start: 0.7932 (mp) cc_final: 0.7374 (tp) REVERT: C 367 ARG cc_start: 0.7569 (OUTLIER) cc_final: 0.7190 (ttt-90) outliers start: 26 outliers final: 15 residues processed: 124 average time/residue: 0.9528 time to fit residues: 127.8348 Evaluate side-chains 122 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 102 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 259 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.1353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 8330 Z= 0.309 Angle : 0.586 10.958 11359 Z= 0.298 Chirality : 0.044 0.200 1329 Planarity : 0.004 0.050 1449 Dihedral : 4.527 28.013 1191 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.80 % Allowed : 19.36 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1098 helix: 1.51 (0.28), residues: 384 sheet: -0.59 (0.29), residues: 291 loop : -0.72 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.004 0.001 HIS H 35 PHE 0.012 0.001 PHE B 241 TYR 0.019 0.002 TYR B 59 ARG 0.005 0.000 ARG C 362 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.937 Fit side-chains REVERT: A 254 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.7951 (tp) REVERT: B 13 GLN cc_start: 0.7546 (tt0) cc_final: 0.7336 (tt0) REVERT: B 46 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7279 (mmm160) REVERT: B 325 MET cc_start: 0.8838 (tpp) cc_final: 0.8353 (mmt) REVERT: H 82 GLN cc_start: 0.8302 (tp40) cc_final: 0.8040 (tp40) REVERT: H 213 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8386 (t) REVERT: C 36 LEU cc_start: 0.7938 (mp) cc_final: 0.7398 (tp) REVERT: C 163 ILE cc_start: 0.7524 (mt) cc_final: 0.7059 (tp) REVERT: C 367 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7181 (ttt-90) outliers start: 22 outliers final: 14 residues processed: 118 average time/residue: 0.9548 time to fit residues: 121.5343 Evaluate side-chains 120 residues out of total 958 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 ILE Chi-restraints excluded: chain B residue 46 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 213 THR Chi-restraints excluded: chain C residue 43 LEU Chi-restraints excluded: chain C residue 157 VAL Chi-restraints excluded: chain C residue 336 ILE Chi-restraints excluded: chain C residue 337 THR Chi-restraints excluded: chain C residue 367 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.0060 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 0.0070 chunk 88 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 76 optimal weight: 0.0050 chunk 4 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 113 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.129868 restraints weight = 8865.102| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 1.86 r_work: 0.3294 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8330 Z= 0.152 Angle : 0.512 8.372 11359 Z= 0.262 Chirality : 0.041 0.180 1329 Planarity : 0.004 0.050 1449 Dihedral : 4.182 23.744 1191 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.04 % Allowed : 20.25 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.26), residues: 1098 helix: 1.72 (0.28), residues: 386 sheet: -0.45 (0.29), residues: 287 loop : -0.58 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 211 HIS 0.002 0.000 HIS B 311 PHE 0.010 0.001 PHE H 27 TYR 0.014 0.001 TYR H 190 ARG 0.004 0.000 ARG C 362 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3081.25 seconds wall clock time: 55 minutes 51.37 seconds (3351.37 seconds total)