Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 16:26:09 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/12_2021/7bz2_30249_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/12_2021/7bz2_30249.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/12_2021/7bz2_30249_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/12_2021/7bz2_30249_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/12_2021/7bz2_30249_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/12_2021/7bz2_30249.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/12_2021/7bz2_30249.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/12_2021/7bz2_30249_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bz2_30249/12_2021/7bz2_30249_updated.pdb" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "R PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 7393 Number of models: 1 Model: "" Number of chains: 5 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: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2177 Unusual residues: {'H98': 1} Classifications: {'undetermined': 1, 'peptide': 285} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 7, 'TRANS': 277, None: 1} Not linked: pdbres="LEU R 340 " pdbres="H98 R 401 " 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 Time building chain proxies: 4.40, per 1000 atoms: 0.60 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 - 3.50 Amimo 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: 2.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 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... running ksdssp... Secondary structure from input PDB file: 27 helices and 9 sheets defined 29.8% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 11 through 13 No H-bonds generated for 'chain 'A' and resid 11 through 13' Processing helix chain 'A' and resid 15 through 37 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 266 through 278 removed outlier: 3.641A pdb=" N SER A 275 " --> pdb=" O ASN A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 4.822A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 388 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 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 16 through 23 Processing helix chain 'G' and resid 30 through 44 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 39 through 59 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 67 through 84 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 87 through 96 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 109 through 136 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 138 through 141 No H-bonds generated for 'chain 'R' and resid 138 through 141' Processing helix chain 'R' and resid 152 through 160 removed outlier: 4.246A pdb=" N ILE R 159 " --> pdb=" O LEU R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 165 No H-bonds generated for 'chain 'R' and resid 162 through 165' Processing helix chain 'R' and resid 167 through 170 No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 181 through 183 No H-bonds generated for 'chain 'R' and resid 181 through 183' Processing helix chain 'R' and resid 199 through 202 No H-bonds generated for 'chain 'R' and resid 199 through 202' Processing helix chain 'R' and resid 204 through 207 No H-bonds generated for 'chain 'R' and resid 204 through 207' Processing helix chain 'R' and resid 210 through 226 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 273 through 298 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) Proline residue: R 288 - end of helix removed outlier: 4.764A pdb=" N ILE R 294 " --> pdb=" O PHE R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 308 No H-bonds generated for 'chain 'R' and resid 305 through 308' Processing helix chain 'R' and resid 311 through 314 No H-bonds generated for 'chain 'R' and resid 311 through 314' Processing helix chain 'R' and resid 322 through 324 No H-bonds generated for 'chain 'R' and resid 322 through 324' Processing helix chain 'R' and resid 330 through 335 Processing sheet with id= A, first strand: chain 'A' and resid 40 through 42 removed outlier: 6.679A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 44 through 46 removed outlier: 3.765A pdb=" N LEU A 46 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.166A pdb=" N TYR A 360 " --> pdb=" O LEU A 289 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N LEU A 291 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N HIS A 362 " --> pdb=" O LEU A 291 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 78 through 82 removed outlier: 3.984A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL B 71 " --> pdb=" O HIS B 62 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 284 through 286 Processing sheet with id= F, 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= G, first strand: chain 'N' and resid 3 through 6 Processing sheet with id= H, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.682A pdb=" N VAL N 12 " --> 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) removed outlier: 3.731A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) Processing sheet with id= I, 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) 179 hydrogen bonds defined for protein. 519 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: 1.58 Time building geometry restraints manager: 3.11 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 1.509 1.391 0.118 2.00e-02 2.50e+03 3.50e+01 bond pdb=" C3 H98 R 401 " pdb=" C4 H98 R 401 " ideal model delta sigma weight residual 1.588 1.480 0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C12 H98 R 401 " pdb=" C13 H98 R 401 " ideal model delta sigma weight residual 1.540 1.496 0.044 2.00e-02 2.50e+03 4.75e+00 bond pdb=" C16 H98 R 401 " pdb=" O2 H98 R 401 " ideal model delta sigma weight residual 1.394 1.356 0.038 2.00e-02 2.50e+03 3.52e+00 bond pdb=" C11 H98 R 401 " pdb=" N1 H98 R 401 " ideal model delta sigma weight residual 1.492 1.458 0.034 2.00e-02 2.50e+03 2.84e+00 ... (remaining 7533 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.53: 140 106.53 - 113.41: 4134 113.41 - 120.28: 2827 120.28 - 127.16: 3065 127.16 - 134.04: 79 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=" 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 angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 121.92 118.31 3.61 1.73e+00 3.34e-01 4.36e+00 ... (remaining 10240 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3938 17.95 - 35.90: 383 35.90 - 53.85: 61 53.85 - 71.81: 13 71.81 - 89.76: 5 Dihedral angle restraints: 4400 sinusoidal: 1561 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 4397 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: 63 0.121 - 0.151: 12 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: 7141 3.22 - 3.78: 10523 3.78 - 4.34: 14194 4.34 - 4.90: 23778 Nonbonded interactions: 55782 Sorted by model distance: nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.101 2.440 nonbonded pdb=" OD2 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.134 2.440 nonbonded pdb=" OG1 THR N 104 " pdb=" OD1 ASP N 106 " model vdw 2.193 2.440 nonbonded pdb=" OD1 ASP B 291 " pdb=" ND2 ASN B 293 " model vdw 2.204 2.520 nonbonded pdb=" OG SER R 203 " pdb=" O2 H98 R 401 " model vdw 2.221 2.440 ... (remaining 55777 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 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. 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 Write .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: 0.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 1.990 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 21.180 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:1.980 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 25.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.118 7538 Z= 0.312 Angle : 0.664 8.137 10245 Z= 0.373 Chirality : 0.046 0.151 1194 Planarity : 0.004 0.050 1295 Dihedral : 14.759 89.757 2552 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.21 % Favored : 89.79 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 *********************** 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 184 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.841 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.1952 time to fit residues: 47.4900 Evaluate side-chains 143 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0833 ------------------------------------------------------------------------------- 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: 2.9990 chunk 72 optimal weight: 0.0040 chunk 39 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 48 optimal weight: 10.0000 chunk 38 optimal weight: 0.3980 chunk 74 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 213 GLN A 371 ASN B 176 GLN B 230 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 13 GLN N 39 GLN R 142 GLN R 148 ASN R 312 ASN R 322 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.069 7538 Z= 0.165 Angle : 0.575 7.997 10245 Z= 0.303 Chirality : 0.043 0.140 1194 Planarity : 0.005 0.093 1295 Dihedral : 5.947 75.411 1046 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer Outliers : 2.72 % 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: -5.03 (0.22), residues: 950 helix: -2.40 (0.25), residues: 354 sheet: -4.34 (0.28), residues: 189 loop : -3.58 (0.23), residues: 407 *********************** 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: 20 poor density : 165 time to evaluate : 0.812 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 11 residues processed: 176 average time/residue: 0.1668 time to fit residues: 40.5116 Evaluate side-chains 158 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 147 time to evaluate : 0.830 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0688 time to fit residues: 2.5425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 71 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 86 optimal weight: 0.3980 chunk 93 optimal weight: 0.0980 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 75 GLN B 176 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 ASN R 170 GLN R 293 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.091 7538 Z= 0.163 Angle : 0.565 9.695 10245 Z= 0.292 Chirality : 0.042 0.144 1194 Planarity : 0.004 0.083 1295 Dihedral : 5.555 73.184 1046 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer Outliers : 2.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.24), residues: 950 helix: -1.92 (0.26), residues: 354 sheet: -3.86 (0.30), residues: 194 loop : -3.11 (0.26), residues: 402 *********************** 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 169 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 148 time to evaluate : 1.055 Fit side-chains outliers start: 21 outliers final: 10 residues processed: 160 average time/residue: 0.1599 time to fit residues: 36.2701 Evaluate side-chains 151 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 141 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0669 time to fit residues: 2.3840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 44 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 82 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 75 GLN B 175 GLN B 183 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 142 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.090 7538 Z= 0.214 Angle : 0.573 8.736 10245 Z= 0.301 Chirality : 0.043 0.137 1194 Planarity : 0.004 0.087 1295 Dihedral : 5.625 74.553 1046 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer Outliers : 2.18 % 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: -4.05 (0.25), residues: 950 helix: -1.70 (0.27), residues: 354 sheet: -3.67 (0.31), residues: 199 loop : -2.92 (0.27), residues: 397 *********************** 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 159 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 143 time to evaluate : 0.867 Fit side-chains outliers start: 16 outliers final: 9 residues processed: 151 average time/residue: 0.1560 time to fit residues: 33.2071 Evaluate side-chains 138 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 0.780 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0646 time to fit residues: 2.1971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 0.5980 chunk 52 optimal weight: 0.0770 chunk 1 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 63 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 82 optimal weight: 30.0000 chunk 23 optimal weight: 6.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 GLN A 371 ASN B 183 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.083 7538 Z= 0.153 Angle : 0.545 8.551 10245 Z= 0.281 Chirality : 0.041 0.140 1194 Planarity : 0.004 0.083 1295 Dihedral : 5.440 74.583 1046 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer Outliers : 1.91 % 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: -3.62 (0.25), residues: 950 helix: -1.34 (0.28), residues: 349 sheet: -3.44 (0.32), residues: 199 loop : -2.68 (0.28), residues: 402 *********************** 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 153 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 139 time to evaluate : 0.831 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 145 average time/residue: 0.1680 time to fit residues: 34.8053 Evaluate side-chains 137 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 130 time to evaluate : 0.769 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0808 time to fit residues: 2.2238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 0.6980 chunk 82 optimal weight: 30.0000 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 42 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 88 optimal weight: 0.4980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 156 GLN B 183 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.099 7538 Z= 0.193 Angle : 0.563 8.021 10245 Z= 0.291 Chirality : 0.042 0.154 1194 Planarity : 0.005 0.088 1295 Dihedral : 5.469 76.585 1046 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer Outliers : 1.50 % 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: -3.38 (0.26), residues: 950 helix: -1.18 (0.28), residues: 354 sheet: -3.32 (0.32), residues: 199 loop : -2.51 (0.28), residues: 397 *********************** 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 148 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 137 time to evaluate : 0.914 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 141 average time/residue: 0.1606 time to fit residues: 31.8791 Evaluate side-chains 135 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 130 time to evaluate : 0.877 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0716 time to fit residues: 1.7563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 67 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 183 HIS ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.342 7538 Z= 0.473 Angle : 0.818 26.261 10245 Z= 0.447 Chirality : 0.044 0.187 1194 Planarity : 0.005 0.092 1295 Dihedral : 5.596 75.914 1046 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.79 % Favored : 92.21 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.11 % 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: -3.41 (0.26), residues: 950 helix: -1.22 (0.28), residues: 355 sheet: -3.31 (0.32), residues: 199 loop : -2.53 (0.28), residues: 396 *********************** 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 154 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 0.844 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 146 average time/residue: 0.1644 time to fit residues: 33.7190 Evaluate side-chains 134 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 127 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0723 time to fit residues: 2.0768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 0.0040 chunk 87 optimal weight: 0.0030 chunk 80 optimal weight: 5.9990 overall best weight: 0.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 371 ASN B 156 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.136 7538 Z= 0.166 Angle : 0.640 13.832 10245 Z= 0.320 Chirality : 0.042 0.164 1194 Planarity : 0.004 0.087 1295 Dihedral : 5.317 74.536 1046 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer Outliers : 1.36 % 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: -3.04 (0.26), residues: 950 helix: -0.86 (0.29), residues: 350 sheet: -3.08 (0.32), residues: 199 loop : -2.37 (0.28), residues: 401 *********************** 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 139 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.830 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 134 average time/residue: 0.1729 time to fit residues: 32.2550 Evaluate side-chains 129 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 123 time to evaluate : 0.840 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0734 time to fit residues: 1.9521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 0.4980 chunk 87 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 0.0570 chunk 90 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.016 0.753 7538 Z= 0.972 Angle : 1.567 106.058 10245 Z= 0.684 Chirality : 0.050 0.570 1194 Planarity : 0.004 0.068 1295 Dihedral : 5.335 74.516 1046 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % Rotamer Outliers : 0.82 % Cbeta Deviations : 0.22 % 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: -3.01 (0.26), residues: 950 helix: -0.83 (0.29), residues: 350 sheet: -3.06 (0.32), residues: 199 loop : -2.37 (0.28), residues: 401 *********************** 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 130 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 0.923 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 128 average time/residue: 0.1740 time to fit residues: 31.1930 Evaluate side-chains 125 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 123 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0764 time to fit residues: 1.4997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 59 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 156 GLN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.016 0.753 7538 Z= 0.974 Angle : 1.567 106.058 10245 Z= 0.687 Chirality : 0.050 0.570 1194 Planarity : 0.005 0.086 1295 Dihedral : 5.335 74.516 1046 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.22 % 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: -3.01 (0.26), residues: 950 helix: -0.83 (0.29), residues: 350 sheet: -3.06 (0.32), residues: 199 loop : -2.37 (0.28), residues: 401 ********************** 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 124 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.843 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.1751 time to fit residues: 30.2247 Evaluate side-chains 123 residues out of total 842 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 20 optimal weight: 7.9990 chunk 75 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 13 optimal weight: 50.0000 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.188286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.166372 restraints weight = 8171.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.163808 restraints weight = 15420.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.156550 restraints weight = 15507.169| |-----------------------------------------------------------------------------| r_work (final): 0.3762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.016 0.753 7538 Z= 0.974 Angle : 1.567 106.056 10245 Z= 0.687 Chirality : 0.050 0.570 1194 Planarity : 0.005 0.086 1295 Dihedral : 5.335 74.516 1046 Min Nonbonded Distance : 1.602 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.84 % Favored : 95.05 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.22 % 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: -3.01 (0.26), residues: 950 helix: -0.83 (0.29), residues: 350 sheet: -3.06 (0.32), residues: 199 loop : -2.37 (0.28), residues: 401 =============================================================================== Job complete usr+sys time: 1510.35 seconds wall clock time: 28 minutes 20.93 seconds (1700.93 seconds total)