Starting phenix.real_space_refine on Fri Dec 8 10:10:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szi_25567/12_2023/7szi_25567.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szi_25567/12_2023/7szi_25567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szi_25567/12_2023/7szi_25567.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szi_25567/12_2023/7szi_25567.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szi_25567/12_2023/7szi_25567.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7szi_25567/12_2023/7szi_25567.pdb" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= 0.025 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 8 5.16 5 C 5058 2.51 5 N 1361 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 2": "OE1" <-> "OE2" Residue "A GLU 57": "OE1" <-> "OE2" Residue "A GLU 66": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 110": "OE1" <-> "OE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A GLU 258": "OE1" <-> "OE2" Residue "A ASP 266": "OD1" <-> "OD2" Residue "B GLU 2": "OE1" <-> "OE2" Residue "B ASP 12": "OD1" <-> "OD2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 110": "OE1" <-> "OE2" Residue "B ASP 114": "OD1" <-> "OD2" Residue "B ASP 136": "OD1" <-> "OD2" Residue "B GLU 217": "OE1" <-> "OE2" Residue "B GLU 258": "OE1" <-> "OE2" Residue "B PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 266": "OD1" <-> "OD2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 8089 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2669 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 338} Chain breaks: 1 Chain: "B" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2695 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 341} Chain: "C" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2665 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 338} Chain breaks: 1 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 60 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 4.63, per 1000 atoms: 0.57 Number of scatterers: 8089 At special positions: 0 Unit cell: (74.52, 95.04, 96.12, 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 8 16.00 O 1662 8.00 N 1361 7.00 C 5058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 0 " - pdb=" SG CYS D 8 " distance=2.94 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.4 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 7.3% alpha, 48.1% 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 98 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 322 through 329 Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.583A pdb=" N GLN C 172 " --> pdb=" O TRP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 322 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 1 through 6 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1 through 6 current: chain 'A' and resid 51 through 61 removed outlier: 6.331A pdb=" N ASN A 59 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR A 74 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN A 61 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA A 72 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 88 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR A 132 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP A 90 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA A 130 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY A 92 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ASN A 215 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA A 242 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A 243 " --> pdb=" O PHE A 250 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE A 250 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N ALA A 251 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU A 283 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG A 270 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA A 300 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER A 272 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 298 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA A 274 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL A 296 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 276 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 294 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER A 278 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 282 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY A 288 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 15 " --> pdb=" O PHE A 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1 through 6 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1 through 6 current: chain 'B' and resid 50 through 61 removed outlier: 6.339A pdb=" N ASN B 59 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR B 74 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLN B 61 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA B 72 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 12.668A pdb=" N ARG B 75 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 95 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER B 88 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR B 132 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP B 90 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA B 130 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY B 92 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 147 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 11.207A pdb=" N ASN B 215 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA B 242 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 243 " --> pdb=" O PHE B 250 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 250 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N ALA B 251 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B 283 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY B 280 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP B 291 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP B 282 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 289 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 1 through 6 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 1 through 6 current: chain 'C' and resid 50 through 61 removed outlier: 6.530A pdb=" N THR C 51 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU C 81 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR C 53 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA C 79 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN C 55 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA C 77 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU C 57 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER C 88 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR C 132 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP C 90 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA C 130 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLY C 92 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N ASN C 215 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA C 242 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR C 231 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR C 263 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA C 233 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ALA C 261 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN C 235 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL C 259 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR C 237 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE C 257 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR C 239 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN C 255 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN C 241 " --> pdb=" O LYS C 253 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS C 253 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR C 243 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N ALA C 251 " --> pdb=" O LEU C 283 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU C 283 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY C 280 " --> pdb=" O ASP C 291 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP C 291 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP C 282 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASP C 289 " --> pdb=" O ASP C 282 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 2.98 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: 2729 1.34 - 1.46: 2197 1.46 - 1.58: 3323 1.58 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 8263 Sorted by residual: bond pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.06e-02 8.90e+03 7.19e-01 bond pdb=" C TYR A 116 " pdb=" N GLY A 117 " ideal model delta sigma weight residual 1.336 1.328 0.008 1.01e-02 9.80e+03 6.36e-01 bond pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.29e-02 6.01e+03 4.90e-01 bond pdb=" CA PHE A 83 " pdb=" CB PHE A 83 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.30e-02 5.92e+03 4.31e-01 bond pdb=" N GLY A 221 " pdb=" CA GLY A 221 " ideal model delta sigma weight residual 1.454 1.448 0.006 9.90e-03 1.02e+04 3.81e-01 ... (remaining 8258 not shown) Histogram of bond angle deviations from ideal: 100.60 - 107.28: 94 107.28 - 113.96: 4264 113.96 - 120.63: 3271 120.63 - 127.31: 3514 127.31 - 133.99: 42 Bond angle restraints: 11185 Sorted by residual: angle pdb=" C TYR A 116 " pdb=" N GLY A 117 " pdb=" CA GLY A 117 " ideal model delta sigma weight residual 122.47 120.21 2.26 8.90e-01 1.26e+00 6.47e+00 angle pdb=" C GLY D 3 " pdb=" N GLN D 4 " pdb=" CA GLN D 4 " ideal model delta sigma weight residual 121.54 125.95 -4.41 1.91e+00 2.74e-01 5.32e+00 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N GLY A 222 " ideal model delta sigma weight residual 115.49 117.81 -2.32 1.03e+00 9.43e-01 5.09e+00 angle pdb=" CA TYR B 58 " pdb=" CB TYR B 58 " pdb=" CG TYR B 58 " ideal model delta sigma weight residual 113.90 117.79 -3.89 1.80e+00 3.09e-01 4.67e+00 angle pdb=" C TYR B 116 " pdb=" N GLY B 117 " pdb=" CA GLY B 117 " ideal model delta sigma weight residual 122.69 120.38 2.31 1.08e+00 8.57e-01 4.58e+00 ... (remaining 11180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 4222 15.35 - 30.70: 352 30.70 - 46.06: 75 46.06 - 61.41: 37 61.41 - 76.76: 5 Dihedral angle restraints: 4691 sinusoidal: 1765 harmonic: 2926 Sorted by residual: dihedral pdb=" CB CYS D 0 " pdb=" SG CYS D 0 " pdb=" SG CYS D 8 " pdb=" CB CYS D 8 " ideal model delta sinusoidal sigma weight residual 93.00 152.84 -59.84 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB LYS C 153 " pdb=" CG LYS C 153 " pdb=" CD LYS C 153 " pdb=" CE LYS C 153 " ideal model delta sinusoidal sigma weight residual 60.00 111.18 -51.18 3 1.50e+01 4.44e-03 8.98e+00 dihedral pdb=" CG LYS A 171 " pdb=" CD LYS A 171 " pdb=" CE LYS A 171 " pdb=" NZ LYS A 171 " ideal model delta sinusoidal sigma weight residual -60.00 -110.97 50.97 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 4688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 626 0.026 - 0.052: 343 0.052 - 0.078: 98 0.078 - 0.105: 40 0.105 - 0.131: 26 Chirality restraints: 1133 Sorted by residual: chirality pdb=" CA VAL B 273 " pdb=" N VAL B 273 " pdb=" C VAL B 273 " pdb=" CB VAL B 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL A 273 " pdb=" N VAL A 273 " pdb=" C VAL A 273 " pdb=" CB VAL A 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL C 273 " pdb=" N VAL C 273 " pdb=" C VAL C 273 " pdb=" CB VAL C 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1130 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 58 " -0.018 2.00e-02 2.50e+03 1.11e-02 2.47e+00 pdb=" CG TYR B 58 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 58 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 58 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 58 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 58 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 58 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 58 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 58 " 0.014 2.00e-02 2.50e+03 8.94e-03 1.60e+00 pdb=" CG TYR C 58 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 58 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 58 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 58 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 58 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 58 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 207 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO C 208 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.015 5.00e-02 4.00e+02 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2113 2.79 - 3.32: 6730 3.32 - 3.85: 13116 3.85 - 4.37: 16407 4.37 - 4.90: 29830 Nonbonded interactions: 68196 Sorted by model distance: nonbonded pdb=" OH TYR B 22 " pdb=" OE2 GLU B 110 " model vdw 2.265 2.440 nonbonded pdb=" OH TYR A 22 " pdb=" OE2 GLU A 110 " model vdw 2.303 2.440 nonbonded pdb=" NH1 ARG B 93 " pdb=" OD1 ASN B 127 " model vdw 2.309 2.520 nonbonded pdb=" OG1 THR C 105 " pdb=" OE2 GLU C 258 " model vdw 2.317 2.440 nonbonded pdb=" ND2 ASN A 252 " pdb=" OE2 GLU A 284 " model vdw 2.328 2.520 ... (remaining 68191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 184 or resid 189 through 344)) selection = (chain 'B' and (resid 0 through 184 or resid 189 through 344)) selection = (chain 'C' and (resid 0 through 184 or resid 189 through 344)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.590 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: 3.410 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.520 Find NCS groups from input model: 0.520 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: 0.010 Load rotamer database and sin/cos tables:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.002 0.027 8263 Z= 0.161 Angle : 0.441 4.406 11185 Z= 0.258 Chirality : 0.038 0.131 1133 Planarity : 0.002 0.026 1505 Dihedral : 13.000 76.760 2878 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 0.12 % Allowed : 0.00 % Favored : 99.88 % 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: 0.36 (0.26), residues: 1026 helix: -0.12 (0.84), residues: 37 sheet: 1.39 (0.22), residues: 510 loop : -1.07 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.002 0.001 HIS B 197 PHE 0.013 0.001 PHE A 137 TYR 0.026 0.001 TYR B 58 ARG 0.002 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.920 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 1.6077 time to fit residues: 98.4556 Evaluate side-chains 50 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.914 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.0950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8263 Z= 0.349 Angle : 0.541 6.299 11185 Z= 0.304 Chirality : 0.042 0.174 1133 Planarity : 0.003 0.033 1505 Dihedral : 4.355 28.711 1155 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 0.36 % Allowed : 4.46 % Favored : 95.18 % 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: 0.44 (0.26), residues: 1026 helix: 0.85 (0.95), residues: 37 sheet: 1.30 (0.22), residues: 528 loop : -1.01 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 56 HIS 0.005 0.001 HIS B 197 PHE 0.015 0.002 PHE A 137 TYR 0.027 0.002 TYR B 58 ARG 0.004 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 1.068 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 50 average time/residue: 1.6795 time to fit residues: 88.7928 Evaluate side-chains 49 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.923 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.9678 time to fit residues: 3.3109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8263 Z= 0.329 Angle : 0.519 5.329 11185 Z= 0.293 Chirality : 0.042 0.175 1133 Planarity : 0.003 0.043 1505 Dihedral : 4.371 30.859 1155 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.70 % Favored : 96.20 % Rotamer: Outliers : 0.72 % Allowed : 6.39 % Favored : 92.89 % 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: 0.37 (0.26), residues: 1026 helix: 0.94 (0.96), residues: 37 sheet: 1.15 (0.21), residues: 540 loop : -1.00 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 56 HIS 0.005 0.002 HIS B 197 PHE 0.015 0.002 PHE C 344 TYR 0.024 0.001 TYR B 58 ARG 0.003 0.000 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.865 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 1.7251 time to fit residues: 96.8222 Evaluate side-chains 52 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 1.1270 time to fit residues: 3.6014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 0.4980 chunk 55 optimal weight: 2.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 8263 Z= 0.423 Angle : 0.548 4.887 11185 Z= 0.308 Chirality : 0.043 0.175 1133 Planarity : 0.003 0.052 1505 Dihedral : 4.542 34.071 1155 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.33 % Allowed : 8.43 % Favored : 90.24 % 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: 0.17 (0.26), residues: 1026 helix: 0.57 (0.88), residues: 43 sheet: 0.99 (0.21), residues: 552 loop : -1.14 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 56 HIS 0.008 0.002 HIS A 197 PHE 0.020 0.002 PHE A 344 TYR 0.024 0.002 TYR B 58 ARG 0.003 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 48 time to evaluate : 0.947 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 55 average time/residue: 1.5535 time to fit residues: 90.6686 Evaluate side-chains 55 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 4 average time/residue: 0.5564 time to fit residues: 3.6923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 68 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8263 Z= 0.341 Angle : 0.515 5.051 11185 Z= 0.291 Chirality : 0.042 0.179 1133 Planarity : 0.003 0.052 1505 Dihedral : 4.424 32.552 1155 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Rotamer: Outliers : 0.96 % Allowed : 10.00 % Favored : 89.04 % 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: 0.14 (0.26), residues: 1026 helix: 0.57 (0.88), residues: 43 sheet: 0.96 (0.21), residues: 550 loop : -1.14 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 56 HIS 0.006 0.002 HIS B 197 PHE 0.020 0.001 PHE A 344 TYR 0.020 0.001 TYR B 58 ARG 0.003 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.954 Fit side-chains outliers start: 8 outliers final: 9 residues processed: 54 average time/residue: 1.5542 time to fit residues: 88.7174 Evaluate side-chains 58 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 49 time to evaluate : 0.827 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 5 average time/residue: 0.8589 time to fit residues: 5.9525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8263 Z= 0.335 Angle : 0.518 4.937 11185 Z= 0.292 Chirality : 0.042 0.175 1133 Planarity : 0.003 0.053 1505 Dihedral : 4.400 31.272 1155 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 0.72 % Allowed : 10.48 % Favored : 88.80 % 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: 0.12 (0.26), residues: 1026 helix: 0.55 (0.88), residues: 43 sheet: 0.95 (0.21), residues: 550 loop : -1.15 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 56 HIS 0.006 0.002 HIS B 197 PHE 0.020 0.001 PHE A 344 TYR 0.020 0.001 TYR B 58 ARG 0.002 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.885 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 1.5594 time to fit residues: 87.6021 Evaluate side-chains 55 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.893 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 2 average time/residue: 0.9607 time to fit residues: 3.2234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8263 Z= 0.325 Angle : 0.512 4.848 11185 Z= 0.289 Chirality : 0.041 0.175 1133 Planarity : 0.003 0.052 1505 Dihedral : 4.366 29.778 1155 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.30 % Rotamer: Outliers : 0.84 % Allowed : 11.57 % Favored : 87.59 % 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: 0.11 (0.26), residues: 1026 helix: 0.55 (0.88), residues: 43 sheet: 0.94 (0.21), residues: 550 loop : -1.14 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 56 HIS 0.006 0.001 HIS B 197 PHE 0.020 0.001 PHE A 344 TYR 0.019 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 49 time to evaluate : 0.892 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 53 average time/residue: 1.6308 time to fit residues: 91.4342 Evaluate side-chains 55 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 0.6461 time to fit residues: 3.3361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 8263 Z= 0.599 Angle : 0.610 5.127 11185 Z= 0.339 Chirality : 0.046 0.178 1133 Planarity : 0.004 0.059 1505 Dihedral : 4.715 33.091 1155 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 0.84 % Allowed : 11.93 % Favored : 87.23 % 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: -0.10 (0.25), residues: 1026 helix: -0.19 (0.81), residues: 49 sheet: 0.83 (0.21), residues: 555 loop : -1.31 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 56 HIS 0.011 0.003 HIS B 197 PHE 0.022 0.002 PHE A 344 TYR 0.025 0.002 TYR B 58 ARG 0.003 0.001 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 45 time to evaluate : 0.947 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 50 average time/residue: 1.6371 time to fit residues: 86.6945 Evaluate side-chains 51 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.926 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.9549 time to fit residues: 3.2768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8263 Z= 0.185 Angle : 0.475 4.625 11185 Z= 0.270 Chirality : 0.040 0.174 1133 Planarity : 0.003 0.051 1505 Dihedral : 4.215 27.506 1155 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Rotamer: Outliers : 0.84 % Allowed : 12.17 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.26), residues: 1026 helix: 0.52 (0.87), residues: 43 sheet: 0.96 (0.21), residues: 534 loop : -1.20 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 73 HIS 0.003 0.001 HIS B 197 PHE 0.021 0.001 PHE A 344 TYR 0.014 0.001 TYR B 58 ARG 0.004 0.000 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.962 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 52 average time/residue: 1.5784 time to fit residues: 86.9034 Evaluate side-chains 54 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.8894 time to fit residues: 3.1335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 8263 Z= 0.456 Angle : 0.557 4.862 11185 Z= 0.312 Chirality : 0.043 0.176 1133 Planarity : 0.003 0.058 1505 Dihedral : 4.517 29.195 1155 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.68 % Favored : 95.22 % Rotamer: Outliers : 0.84 % Allowed : 12.41 % Favored : 86.75 % 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: 0.02 (0.26), residues: 1026 helix: 0.54 (0.88), residues: 43 sheet: 0.85 (0.21), residues: 552 loop : -1.18 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 56 HIS 0.008 0.002 HIS B 197 PHE 0.020 0.002 PHE A 344 TYR 0.022 0.002 TYR B 58 ARG 0.002 0.000 ARG C 37 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.854 Fit side-chains outliers start: 7 outliers final: 7 residues processed: 52 average time/residue: 1.6030 time to fit residues: 88.1363 Evaluate side-chains 54 residues out of total 830 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 2 average time/residue: 0.9715 time to fit residues: 3.2002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 58 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 GLN ** B 173 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 = 0.2857 r_free = 0.2857 target = 0.072098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.059725 restraints weight = 14175.684| |-----------------------------------------------------------------------------| r_work (start): 0.2616 rms_B_bonded: 2.41 r_work: 0.2505 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8263 Z= 0.257 Angle : 0.493 4.693 11185 Z= 0.279 Chirality : 0.041 0.174 1133 Planarity : 0.003 0.056 1505 Dihedral : 4.277 26.339 1155 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Rotamer: Outliers : 0.84 % Allowed : 12.41 % Favored : 86.75 % 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: 0.03 (0.26), residues: 1026 helix: 0.53 (0.88), residues: 43 sheet: 0.93 (0.21), residues: 534 loop : -1.20 (0.28), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 56 HIS 0.004 0.001 HIS B 197 PHE 0.021 0.001 PHE A 344 TYR 0.016 0.001 TYR B 58 ARG 0.002 0.000 ARG A 167 =============================================================================== Job complete usr+sys time: 2441.17 seconds wall clock time: 44 minutes 48.96 seconds (2688.96 seconds total)