Starting phenix.real_space_refine on Tue Sep 24 07:21:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/09_2024/7bz2_30249.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/09_2024/7bz2_30249.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/09_2024/7bz2_30249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/09_2024/7bz2_30249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/09_2024/7bz2_30249.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/09_2024/7bz2_30249.cif" } resolution = 3.82 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= 0.005 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 44 5.16 5 C 4725 2.51 5 N 1275 2.21 5 O 1349 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 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: 7393 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1561 Classifications: {'peptide': 198} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 3, 'TRANS': 194} Chain breaks: 5 Unresolved non-hydrogen bonds: 123 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 7, 'GLU:plan': 4, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2453 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 325} Chain breaks: 2 Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 3, 'ARG:plan': 6, 'ASN:plan1': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 73 Chain: "G" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 246 Classifications: {'peptide': 37} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 1, 'TRANS': 35} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "N" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 956 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "R" Number of atoms: 2152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2152 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 277} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 197 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 102 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'H98': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.64, per 1000 atoms: 0.63 Number of scatterers: 7393 At special positions: 0 Unit cell: (92.22, 96.46, 117.66, 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 44 16.00 O 1349 8.00 N 1275 7.00 C 4725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 1.72 Conformation dependent library (CDL) restraints added in 986.0 milliseconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1842 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 12 sheets defined 33.8% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 10 through 13 Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.705A pdb=" N ALA A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N GLN A 31 " --> pdb=" O GLU A 27 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 279 removed outlier: 3.628A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.697A pdb=" N PHE A 315 " --> pdb=" O PHE A 312 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 332 through 350 removed outlier: 4.822A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 389 removed outlier: 3.959A pdb=" N ASP A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASP A 381 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ILE A 382 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE A 383 " --> pdb=" O CYS A 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 25 Processing helix chain 'G' and resid 16 through 24 Processing helix chain 'G' and resid 29 through 45 removed outlier: 4.199A pdb=" N ALA G 35 " --> pdb=" O SER G 31 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 60 removed outlier: 3.822A pdb=" N ILE R 43 " --> pdb=" O VAL R 39 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL R 44 " --> pdb=" O MET R 40 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL R 52 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE R 58 " --> pdb=" O VAL R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 85 removed outlier: 4.070A pdb=" N PHE R 71 " --> pdb=" O VAL R 67 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR R 73 " --> pdb=" O ASN R 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA R 78 " --> pdb=" O SER R 74 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP R 79 " --> pdb=" O LEU R 75 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N MET R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 86 through 97 removed outlier: 3.579A pdb=" N ALA R 92 " --> pdb=" O PRO R 88 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE R 94 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 137 removed outlier: 3.671A pdb=" N VAL R 114 " --> pdb=" O THR R 110 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU R 115 " --> pdb=" O SER R 111 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR R 118 " --> pdb=" O VAL R 114 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU R 124 " --> pdb=" O SER R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 142 removed outlier: 4.698A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 153 through 161 removed outlier: 4.246A pdb=" N ILE R 159 " --> pdb=" O LEU R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 161 through 166 Processing helix chain 'R' and resid 166 through 171 Processing helix chain 'R' and resid 198 through 203 removed outlier: 3.954A pdb=" N ALA R 202 " --> pdb=" O ALA R 198 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 208 Processing helix chain 'R' and resid 209 through 227 removed outlier: 3.915A pdb=" N VAL R 213 " --> pdb=" O TYR R 209 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR R 219 " --> pdb=" O MET R 215 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU R 225 " --> pdb=" O ARG R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 232 through 236 removed outlier: 3.545A pdb=" N LYS R 235 " --> pdb=" O LYS R 232 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 287 removed outlier: 4.915A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ALA R 285 " --> pdb=" O THR R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 299 removed outlier: 4.764A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 309 Processing helix chain 'R' and resid 310 through 315 Processing helix chain 'R' and resid 321 through 325 Processing helix chain 'R' and resid 329 through 336 Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42 removed outlier: 7.346A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.765A pdb=" N LEU A 46 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL A 247 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE A 246 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU A 289 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS A 362 " --> pdb=" O LEU A 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.645A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 Processing sheet with id=AA5, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.844A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 200 through 201 removed outlier: 3.713A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232 removed outlier: 4.145A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 250 through 253 removed outlier: 3.715A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 277 removed outlier: 4.180A pdb=" N SER B 277 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 6 Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.194A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'N' and resid 17 through 20 removed outlier: 3.512A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 624 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: 1.77 Time building geometry restraints manager: 1.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2395 1.34 - 1.46: 1787 1.46 - 1.58: 3294 1.58 - 1.70: 0 1.70 - 1.81: 62 Bond restraints: 7538 Sorted by residual: bond pdb=" C19 H98 R 401 " pdb=" N2 H98 R 401 " ideal model delta sigma weight residual 1.349 1.391 -0.042 2.00e-02 2.50e+03 4.36e+00 bond pdb=" C3 H98 R 401 " pdb=" C4 H98 R 401 " ideal model delta sigma weight residual 1.503 1.480 0.023 2.00e-02 2.50e+03 1.31e+00 bond pdb=" C13 H98 R 401 " pdb=" C14 H98 R 401 " ideal model delta sigma weight residual 1.392 1.370 0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" CA GLY A 47 " pdb=" C GLY A 47 " ideal model delta sigma weight residual 1.514 1.499 0.015 1.41e-02 5.03e+03 1.19e+00 bond pdb=" CB TRP B 82 " pdb=" CG TRP B 82 " ideal model delta sigma weight residual 1.498 1.465 0.033 3.10e-02 1.04e+03 1.13e+00 ... (remaining 7533 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 9945 1.68 - 3.35: 251 3.35 - 5.03: 37 5.03 - 6.70: 9 6.70 - 8.38: 3 Bond angle restraints: 10245 Sorted by residual: angle pdb=" N VAL R 31 " pdb=" CA VAL R 31 " pdb=" C VAL R 31 " ideal model delta sigma weight residual 113.53 109.98 3.55 9.80e-01 1.04e+00 1.31e+01 angle pdb=" C GLU B 172 " pdb=" N THR B 173 " pdb=" CA THR B 173 " ideal model delta sigma weight residual 121.54 128.13 -6.59 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C15 H98 R 401 " pdb=" N2 H98 R 401 " pdb=" C19 H98 R 401 " ideal model delta sigma weight residual 129.13 120.75 8.38 3.00e+00 1.11e-01 7.80e+00 angle pdb=" N GLY B 162 " pdb=" CA GLY B 162 " pdb=" C GLY B 162 " ideal model delta sigma weight residual 113.18 107.08 6.10 2.37e+00 1.78e-01 6.62e+00 angle pdb=" CA LEU A 393 " pdb=" CB LEU A 393 " pdb=" CG LEU A 393 " ideal model delta sigma weight residual 116.30 124.44 -8.14 3.50e+00 8.16e-02 5.40e+00 ... (remaining 10240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3942 17.95 - 35.90: 383 35.90 - 53.85: 64 53.85 - 71.81: 17 71.81 - 89.76: 6 Dihedral angle restraints: 4412 sinusoidal: 1573 harmonic: 2839 Sorted by residual: dihedral pdb=" CA PHE R 290 " pdb=" C PHE R 290 " pdb=" N ILE R 291 " pdb=" CA ILE R 291 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CB CYS R 184 " pdb=" SG CYS R 184 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual -86.00 -47.65 -38.35 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CA ASN R 69 " pdb=" C ASN R 69 " pdb=" N TYR R 70 " pdb=" CA TYR R 70 " ideal model delta harmonic sigma weight residual 180.00 157.62 22.38 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 627 0.030 - 0.060: 364 0.060 - 0.091: 128 0.091 - 0.121: 64 0.121 - 0.151: 11 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CG LEU A 291 " pdb=" CB LEU A 291 " pdb=" CD1 LEU A 291 " pdb=" CD2 LEU A 291 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.70e-01 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.02e-01 chirality pdb=" CA TYR R 219 " pdb=" N TYR R 219 " pdb=" C TYR R 219 " pdb=" CB TYR R 219 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.81e-01 ... (remaining 1191 not shown) Planarity restraints: 1295 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 167 " -0.033 5.00e-02 4.00e+02 5.02e-02 4.03e+00 pdb=" N PRO R 168 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO R 168 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 168 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.032 5.00e-02 4.00e+02 4.86e-02 3.79e+00 pdb=" N PRO B 236 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " 0.024 5.00e-02 4.00e+02 3.64e-02 2.12e+00 pdb=" N PRO N 88 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " 0.020 5.00e-02 4.00e+02 ... (remaining 1292 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 146 2.66 - 3.22: 7103 3.22 - 3.78: 10470 3.78 - 4.34: 14131 4.34 - 4.90: 23768 Nonbonded interactions: 55618 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.101 3.040 nonbonded pdb=" OD2 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.134 3.040 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.193 3.040 nonbonded pdb=" OD1 ASP B 291 " pdb=" ND2 ASN B 293 " model vdw 2.204 3.120 nonbonded pdb=" OG SER R 203 " pdb=" O2 H98 R 401 " model vdw 2.221 3.040 ... (remaining 55613 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=1.00 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: 0.360 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.600 Find NCS groups from input model: 0.080 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 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 0.042 7538 Z= 0.279 Angle : 0.680 8.376 10245 Z= 0.376 Chirality : 0.046 0.151 1194 Planarity : 0.004 0.050 1295 Dihedral : 15.119 89.757 2564 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.04 (0.20), residues: 950 helix: -3.35 (0.21), residues: 342 sheet: -4.69 (0.26), residues: 190 loop : -4.15 (0.21), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 109 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.002 PHE N 108 TYR 0.013 0.001 TYR B 59 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: B 111 TYR cc_start: 0.7918 (m-80) cc_final: 0.7697 (m-80) REVERT: R 227 LYS cc_start: 0.8479 (ttpt) cc_final: 0.7850 (tttt) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2054 time to fit residues: 49.8415 Evaluate side-chains 144 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 0.0050 chunk 86 optimal weight: 0.8980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN A 220 HIS A 371 ASN B 176 GLN B 230 ASN N 39 GLN R 142 GLN R 148 ASN R 312 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7538 Z= 0.171 Angle : 0.587 8.282 10245 Z= 0.309 Chirality : 0.044 0.137 1194 Planarity : 0.004 0.048 1295 Dihedral : 7.534 82.044 1058 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.32 % Allowed : 17.71 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.23), residues: 950 helix: -2.38 (0.25), residues: 342 sheet: -4.24 (0.29), residues: 187 loop : -3.44 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 313 HIS 0.005 0.001 HIS B 311 PHE 0.030 0.002 PHE R 208 TYR 0.013 0.001 TYR G 40 ARG 0.005 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 0.786 Fit side-chains REVERT: A 45 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8359 (tt) REVERT: B 111 TYR cc_start: 0.7824 (m-80) cc_final: 0.7221 (m-80) REVERT: B 154 ASP cc_start: 0.7937 (m-30) cc_final: 0.7338 (t0) REVERT: N 83 MET cc_start: 0.7294 (mtp) cc_final: 0.7081 (mtp) outliers start: 17 outliers final: 10 residues processed: 178 average time/residue: 0.1866 time to fit residues: 44.9921 Evaluate side-chains 160 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 312 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 71 optimal weight: 0.2980 chunk 58 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 176 GLN B 183 HIS B 220 GLN R 142 GLN R 148 ASN R 170 GLN R 293 ASN R 312 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7538 Z= 0.157 Angle : 0.565 8.541 10245 Z= 0.294 Chirality : 0.042 0.142 1194 Planarity : 0.003 0.047 1295 Dihedral : 6.993 87.082 1058 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.81 % Allowed : 19.35 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.24), residues: 950 helix: -1.97 (0.26), residues: 351 sheet: -3.80 (0.30), residues: 192 loop : -3.06 (0.26), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 109 HIS 0.004 0.001 HIS R 296 PHE 0.018 0.001 PHE A 222 TYR 0.008 0.001 TYR G 40 ARG 0.006 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 0.817 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8416 (tt) REVERT: B 111 TYR cc_start: 0.7785 (m-80) cc_final: 0.7313 (m-80) REVERT: B 147 SER cc_start: 0.8669 (t) cc_final: 0.8437 (t) REVERT: B 154 ASP cc_start: 0.7928 (m-30) cc_final: 0.7375 (t0) REVERT: B 188 MET cc_start: 0.8402 (mmp) cc_final: 0.7910 (mmm) REVERT: R 300 ASP cc_start: 0.7735 (OUTLIER) cc_final: 0.7171 (m-30) outliers start: 28 outliers final: 13 residues processed: 169 average time/residue: 0.1632 time to fit residues: 38.4239 Evaluate side-chains 150 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 175 GLN B 176 GLN B 183 HIS N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7538 Z= 0.162 Angle : 0.547 8.278 10245 Z= 0.286 Chirality : 0.042 0.135 1194 Planarity : 0.003 0.045 1295 Dihedral : 6.755 86.531 1058 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.95 % Allowed : 21.53 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.25), residues: 950 helix: -1.60 (0.27), residues: 348 sheet: -3.55 (0.31), residues: 199 loop : -2.74 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.014 0.001 PHE R 193 TYR 0.008 0.001 TYR G 40 ARG 0.005 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 0.816 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8414 (tt) REVERT: B 111 TYR cc_start: 0.7760 (m-80) cc_final: 0.7300 (m-80) REVERT: B 154 ASP cc_start: 0.7928 (m-30) cc_final: 0.7351 (t0) REVERT: R 36 MET cc_start: 0.6906 (mmt) cc_final: 0.6471 (mmm) REVERT: R 64 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6863 (mt) REVERT: R 300 ASP cc_start: 0.7627 (OUTLIER) cc_final: 0.6915 (m-30) REVERT: R 309 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8422 (tt) outliers start: 29 outliers final: 15 residues processed: 153 average time/residue: 0.1690 time to fit residues: 35.6751 Evaluate side-chains 143 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 205 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 300 ASP Chi-restraints excluded: chain R residue 309 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.9990 chunk 52 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 82 optimal weight: 8.9990 chunk 23 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 176 GLN B 183 HIS N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7538 Z= 0.150 Angle : 0.537 8.111 10245 Z= 0.277 Chirality : 0.042 0.161 1194 Planarity : 0.003 0.044 1295 Dihedral : 6.472 85.661 1058 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 4.36 % Allowed : 23.57 % Favored : 72.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.25), residues: 950 helix: -1.31 (0.27), residues: 345 sheet: -3.36 (0.31), residues: 201 loop : -2.60 (0.28), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.012 0.001 PHE A 212 TYR 0.009 0.001 TYR G 40 ARG 0.005 0.000 ARG R 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: A 45 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8424 (tt) REVERT: B 256 ARG cc_start: 0.7112 (mmm160) cc_final: 0.6716 (mtm180) REVERT: N 60 TYR cc_start: 0.8751 (m-80) cc_final: 0.8392 (m-80) REVERT: R 64 LEU cc_start: 0.7203 (OUTLIER) cc_final: 0.6857 (mt) REVERT: R 300 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.6819 (m-30) outliers start: 32 outliers final: 16 residues processed: 153 average time/residue: 0.1619 time to fit residues: 34.6704 Evaluate side-chains 144 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 73 ASP Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 7 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 183 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7538 Z= 0.178 Angle : 0.553 8.172 10245 Z= 0.285 Chirality : 0.043 0.142 1194 Planarity : 0.003 0.044 1295 Dihedral : 6.398 81.353 1058 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.68 % Allowed : 24.93 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.26 (0.26), residues: 950 helix: -1.11 (0.28), residues: 351 sheet: -3.15 (0.33), residues: 199 loop : -2.45 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.013 0.001 PHE A 222 TYR 0.017 0.001 TYR B 111 ARG 0.005 0.000 ARG R 304 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 0.794 Fit side-chains REVERT: A 45 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8436 (tt) REVERT: A 212 PHE cc_start: 0.7261 (p90) cc_final: 0.6999 (p90) REVERT: B 88 ASN cc_start: 0.8641 (m-40) cc_final: 0.8136 (m110) REVERT: B 111 TYR cc_start: 0.7522 (m-80) cc_final: 0.7082 (m-80) REVERT: B 154 ASP cc_start: 0.7635 (m-30) cc_final: 0.7274 (t0) REVERT: N 60 TYR cc_start: 0.8711 (m-80) cc_final: 0.8408 (m-80) REVERT: R 64 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6914 (mt) REVERT: R 300 ASP cc_start: 0.7482 (OUTLIER) cc_final: 0.6826 (m-30) outliers start: 27 outliers final: 18 residues processed: 150 average time/residue: 0.1985 time to fit residues: 41.1999 Evaluate side-chains 147 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 126 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 206 VAL Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 0.2980 chunk 67 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 chunk 91 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 36 optimal weight: 0.0370 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7538 Z= 0.131 Angle : 0.534 7.607 10245 Z= 0.273 Chirality : 0.042 0.151 1194 Planarity : 0.003 0.044 1295 Dihedral : 6.130 79.073 1058 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 4.09 % Allowed : 24.93 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.27), residues: 950 helix: -0.70 (0.29), residues: 344 sheet: -2.90 (0.34), residues: 198 loop : -2.27 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 313 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE A 222 TYR 0.011 0.001 TYR B 111 ARG 0.007 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8417 (tt) REVERT: A 212 PHE cc_start: 0.7214 (p90) cc_final: 0.6988 (p90) REVERT: B 111 TYR cc_start: 0.7631 (m-80) cc_final: 0.7314 (m-80) REVERT: B 154 ASP cc_start: 0.7597 (m-30) cc_final: 0.7293 (t0) REVERT: N 35 ASN cc_start: 0.8326 (p0) cc_final: 0.7794 (p0) REVERT: N 60 TYR cc_start: 0.8685 (m-80) cc_final: 0.8396 (m-80) REVERT: R 64 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6823 (mt) REVERT: R 300 ASP cc_start: 0.7354 (OUTLIER) cc_final: 0.6736 (m-30) outliers start: 30 outliers final: 20 residues processed: 147 average time/residue: 0.1750 time to fit residues: 35.3384 Evaluate side-chains 143 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 110 VAL Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 5.9990 chunk 27 optimal weight: 0.0040 chunk 17 optimal weight: 0.3980 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 0.0070 chunk 80 optimal weight: 5.9990 overall best weight: 0.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7538 Z= 0.134 Angle : 0.542 10.670 10245 Z= 0.275 Chirality : 0.042 0.139 1194 Planarity : 0.003 0.044 1295 Dihedral : 6.010 76.297 1058 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 3.13 % Allowed : 25.89 % Favored : 70.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.27), residues: 950 helix: -0.49 (0.29), residues: 345 sheet: -2.64 (0.33), residues: 208 loop : -2.21 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 109 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE N 103 TYR 0.009 0.001 TYR G 40 ARG 0.006 0.000 ARG R 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 124 time to evaluate : 0.851 Fit side-chains revert: symmetry clash REVERT: A 45 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8402 (tt) REVERT: A 212 PHE cc_start: 0.7196 (p90) cc_final: 0.6982 (p90) REVERT: B 111 TYR cc_start: 0.7518 (m-80) cc_final: 0.7156 (m-80) REVERT: B 154 ASP cc_start: 0.7627 (m-30) cc_final: 0.7333 (t0) REVERT: B 188 MET cc_start: 0.8223 (mmp) cc_final: 0.7918 (mmm) REVERT: N 35 ASN cc_start: 0.8340 (p0) cc_final: 0.7868 (p0) REVERT: N 60 TYR cc_start: 0.8671 (m-80) cc_final: 0.8449 (m-80) REVERT: R 64 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6809 (mt) REVERT: R 300 ASP cc_start: 0.7369 (OUTLIER) cc_final: 0.6842 (m-30) outliers start: 23 outliers final: 14 residues processed: 138 average time/residue: 0.1692 time to fit residues: 32.3820 Evaluate side-chains 131 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 67 optimal weight: 0.0770 chunk 26 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7538 Z= 0.151 Angle : 0.567 9.737 10245 Z= 0.283 Chirality : 0.042 0.148 1194 Planarity : 0.003 0.044 1295 Dihedral : 6.016 80.211 1058 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.27 % Allowed : 26.57 % Favored : 70.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.27), residues: 950 helix: -0.43 (0.29), residues: 345 sheet: -2.57 (0.33), residues: 214 loop : -2.17 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP B 82 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE N 103 TYR 0.009 0.001 TYR G 40 ARG 0.009 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 119 time to evaluate : 0.842 Fit side-chains REVERT: A 45 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8421 (tt) REVERT: A 212 PHE cc_start: 0.7200 (p90) cc_final: 0.6995 (p90) REVERT: B 88 ASN cc_start: 0.8671 (m-40) cc_final: 0.8173 (m110) REVERT: B 111 TYR cc_start: 0.7548 (m-80) cc_final: 0.7209 (m-80) REVERT: B 154 ASP cc_start: 0.7658 (m-30) cc_final: 0.7333 (t0) REVERT: B 188 MET cc_start: 0.8265 (mmp) cc_final: 0.7974 (mmm) REVERT: N 60 TYR cc_start: 0.8667 (m-80) cc_final: 0.8432 (m-80) REVERT: R 64 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6843 (mt) REVERT: R 140 LYS cc_start: 0.7638 (mtpp) cc_final: 0.7217 (mtmm) REVERT: R 300 ASP cc_start: 0.7316 (OUTLIER) cc_final: 0.6845 (m-30) outliers start: 24 outliers final: 15 residues processed: 135 average time/residue: 0.1697 time to fit residues: 32.1540 Evaluate side-chains 132 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 110 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7538 Z= 0.163 Angle : 0.584 8.786 10245 Z= 0.293 Chirality : 0.043 0.180 1194 Planarity : 0.003 0.044 1295 Dihedral : 6.009 84.116 1058 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.41 % Allowed : 26.57 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.27), residues: 950 helix: -0.46 (0.29), residues: 354 sheet: -2.55 (0.33), residues: 216 loop : -2.13 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 82 HIS 0.003 0.001 HIS B 54 PHE 0.011 0.001 PHE N 103 TYR 0.009 0.001 TYR B 59 ARG 0.008 0.000 ARG B 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 120 time to evaluate : 0.807 Fit side-chains REVERT: A 45 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8428 (tt) REVERT: A 212 PHE cc_start: 0.7208 (p90) cc_final: 0.6996 (p90) REVERT: B 88 ASN cc_start: 0.8660 (m-40) cc_final: 0.8264 (m110) REVERT: B 111 TYR cc_start: 0.7514 (m-80) cc_final: 0.7169 (m-80) REVERT: B 154 ASP cc_start: 0.7689 (m-30) cc_final: 0.7395 (t0) REVERT: N 60 TYR cc_start: 0.8627 (m-80) cc_final: 0.8387 (m-80) REVERT: R 64 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6897 (mt) REVERT: R 140 LYS cc_start: 0.7634 (mtpp) cc_final: 0.7184 (mtmm) REVERT: R 300 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6806 (m-30) outliers start: 25 outliers final: 16 residues processed: 136 average time/residue: 0.1792 time to fit residues: 33.4997 Evaluate side-chains 136 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 117 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 44 HIS Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 159 ILE Chi-restraints excluded: chain R residue 218 VAL Chi-restraints excluded: chain R residue 281 THR Chi-restraints excluded: chain R residue 300 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 20 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 31 optimal weight: 20.0000 chunk 77 optimal weight: 0.7980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.0670 chunk 66 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 54 optimal weight: 5.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.179659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.151760 restraints weight = 8101.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.148538 restraints weight = 11300.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.150843 restraints weight = 10710.938| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7538 Z= 0.144 Angle : 0.590 8.759 10245 Z= 0.292 Chirality : 0.042 0.148 1194 Planarity : 0.003 0.044 1295 Dihedral : 5.938 89.081 1058 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.00 % Allowed : 26.98 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.27), residues: 950 helix: -0.34 (0.29), residues: 354 sheet: -2.52 (0.33), residues: 215 loop : -2.04 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 82 HIS 0.003 0.001 HIS R 296 PHE 0.013 0.001 PHE N 103 TYR 0.008 0.001 TYR G 40 ARG 0.010 0.000 ARG R 304 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.23 seconds wall clock time: 31 minutes 37.01 seconds (1897.01 seconds total)