Starting phenix.real_space_refine on Mon Mar 11 14:20:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/03_2024/8kae_37008_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/03_2024/8kae_37008.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/03_2024/8kae_37008_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/03_2024/8kae_37008_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/03_2024/8kae_37008_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/03_2024/8kae_37008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/03_2024/8kae_37008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/03_2024/8kae_37008_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/03_2024/8kae_37008_updated.pdb" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.108 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 41 5.16 5 C 5393 2.51 5 N 1412 2.21 5 O 1594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 10": "OE1" <-> "OE2" Residue "H PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 66": "OD1" <-> "OD2" Residue "H TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 47": "OE1" <-> "OE2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 88": "OE1" <-> "OE2" Residue "N ASP 91": "OD1" <-> "OD2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 102": "OE1" <-> "OE2" Residue "N TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 118": "OD1" <-> "OD2" Residue "R TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 147": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 163": "OD1" <-> "OD2" Residue "R PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 246": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 375": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 437": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 492": "OD1" <-> "OD2" Residue "R TYR 503": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 518": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 529": "OD1" <-> "OD2" Residue "R GLU 534": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8440 Number of models: 1 Model: "" Number of chains: 6 Chain: "H" Number of atoms: 1732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1732 Classifications: {'peptide': 229} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 217} Chain: "K" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 922 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1619 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 202} Chain: "N" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 959 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 119} Chain: "R" Number of atoms: 3183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3183 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 12, 'TRANS': 404} Chain breaks: 2 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'YUX': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.60 Number of scatterers: 8440 At special positions: 0 Unit cell: (78.1, 89.1, 163.9, 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 41 16.00 O 1594 8.00 N 1412 7.00 C 5393 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 26 " - pdb=" SG CYS H 100 " distance=2.05 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 215 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 90 " distance=2.05 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 97 " distance=2.05 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: 3.27 Conformation dependent library (CDL) restraints added in 1.8 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2010 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 14 sheets defined 33.9% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'H' and resid 33 through 35 No H-bonds generated for 'chain 'H' and resid 33 through 35' Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 174 through 176 No H-bonds generated for 'chain 'H' and resid 174 through 176' Processing helix chain 'H' and resid 205 through 210 Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'L' and resid 124 through 129 removed outlier: 3.730A pdb=" N SER L 129 " --> pdb=" O SER L 125 " (cutoff:3.500A) Processing helix chain 'L' and resid 185 through 190 removed outlier: 3.888A pdb=" N LYS L 190 " --> pdb=" O ALA L 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 91 No H-bonds generated for 'chain 'N' and resid 89 through 91' Processing helix chain 'R' and resid 101 through 117 Processing helix chain 'R' and resid 123 through 133 removed outlier: 5.730A pdb=" N LEU R 127 " --> pdb=" O GLY R 124 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN R 130 " --> pdb=" O LEU R 127 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE R 133 " --> pdb=" O GLN R 130 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 162 removed outlier: 3.989A pdb=" N LEU R 142 " --> pdb=" O ARG R 138 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU R 143 " --> pdb=" O GLY R 139 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N GLN R 144 " --> pdb=" O ALA R 140 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE R 147 " --> pdb=" O LEU R 143 " (cutoff:3.500A) Proline residue: R 156 - end of helix removed outlier: 3.526A pdb=" N GLY R 162 " --> pdb=" O PHE R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 187 removed outlier: 3.993A pdb=" N SER R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N PHE R 187 " --> pdb=" O PHE R 183 " (cutoff:3.500A) Processing helix chain 'R' and resid 194 through 219 Proline residue: R 215 - end of helix Processing helix chain 'R' and resid 227 through 256 removed outlier: 4.075A pdb=" N ALA R 237 " --> pdb=" O VAL R 233 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N ILE R 238 " --> pdb=" O PHE R 234 " (cutoff:3.500A) Proline residue: R 239 - end of helix removed outlier: 3.922A pdb=" N TYR R 246 " --> pdb=" O SER R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 263 Processing helix chain 'R' and resid 266 through 278 removed outlier: 4.209A pdb=" N LEU R 278 " --> pdb=" O GLY R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 311 removed outlier: 3.606A pdb=" N LYS R 307 " --> pdb=" O LEU R 303 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA R 308 " --> pdb=" O ARG R 304 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ARG R 311 " --> pdb=" O LYS R 307 " (cutoff:3.500A) Processing helix chain 'R' and resid 313 through 346 removed outlier: 3.968A pdb=" N VAL R 325 " --> pdb=" O ALA R 321 " (cutoff:3.500A) Proline residue: R 337 - end of helix Processing helix chain 'R' and resid 363 through 390 removed outlier: 3.936A pdb=" N PHE R 372 " --> pdb=" O ALA R 368 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N PHE R 375 " --> pdb=" O CYS R 371 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL R 378 " --> pdb=" O GLY R 374 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N LEU R 390 " --> pdb=" O ARG R 386 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 411 Processing helix chain 'R' and resid 414 through 419 removed outlier: 5.974A pdb=" N LYS R 419 " --> pdb=" O PHE R 415 " (cutoff:3.500A) Processing helix chain 'R' and resid 423 through 436 Processing helix chain 'R' and resid 443 through 449 removed outlier: 3.737A pdb=" N TYR R 449 " --> pdb=" O ASP R 445 " (cutoff:3.500A) Processing helix chain 'R' and resid 457 through 469 Processing helix chain 'R' and resid 475 through 489 removed outlier: 4.017A pdb=" N SER R 489 " --> pdb=" O LEU R 485 " (cutoff:3.500A) Processing helix chain 'R' and resid 494 through 540 removed outlier: 3.891A pdb=" N MET R 506 " --> pdb=" O GLY R 502 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU R 507 " --> pdb=" O TYR R 503 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N CYS R 508 " --> pdb=" O ALA R 504 " (cutoff:3.500A) Proline residue: R 509 - end of helix removed outlier: 4.001A pdb=" N PHE R 525 " --> pdb=" O ALA R 521 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N VAL R 527 " --> pdb=" O ALA R 523 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N SER R 528 " --> pdb=" O LEU R 524 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'H' and resid 7 through 11 Processing sheet with id= B, first strand: chain 'H' and resid 14 through 16 removed outlier: 6.322A pdb=" N ARG H 42 " --> pdb=" O TRP H 51 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N TRP H 51 " --> pdb=" O ARG H 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 139 through 143 removed outlier: 5.955A pdb=" N TYR H 195 " --> pdb=" O ASP H 163 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 169 through 173 Processing sheet with id= E, first strand: chain 'K' and resid 3 through 7 Processing sheet with id= F, first strand: chain 'K' and resid 10 through 12 removed outlier: 5.392A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'K' and resid 97 through 99 removed outlier: 4.346A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 7 through 9 Processing sheet with id= I, first strand: chain 'L' and resid 12 through 14 removed outlier: 6.473A pdb=" N LYS L 105 " --> pdb=" O LEU L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'L' and resid 87 through 91 removed outlier: 6.084A pdb=" N GLN L 39 " --> pdb=" O LEU L 48 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU L 48 " --> pdb=" O GLN L 39 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 116 through 120 removed outlier: 6.128A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 146 through 151 Processing sheet with id= M, first strand: chain 'N' and resid 4 through 7 Processing sheet with id= N, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.086A pdb=" N ARG N 39 " --> pdb=" O GLY N 48 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N GLY N 48 " --> pdb=" O ARG N 39 " (cutoff:3.500A) 418 hydrogen bonds defined for protein. 1146 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: 2.79 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2227 1.33 - 1.45: 2073 1.45 - 1.58: 4278 1.58 - 1.70: 0 1.70 - 1.83: 59 Bond restraints: 8637 Sorted by residual: bond pdb=" C07 YUX R 601 " pdb=" N06 YUX R 601 " ideal model delta sigma weight residual 1.342 1.440 -0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" CB VAL N 94 " pdb=" CG1 VAL N 94 " ideal model delta sigma weight residual 1.521 1.431 0.090 3.30e-02 9.18e+02 7.43e+00 bond pdb=" C SER L 95 " pdb=" N SER L 96 " ideal model delta sigma weight residual 1.332 1.297 0.036 1.40e-02 5.10e+03 6.47e+00 bond pdb=" CB VAL N 94 " pdb=" CG2 VAL N 94 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.10e+00 bond pdb=" CB GLU R 207 " pdb=" CG GLU R 207 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.67e+00 ... (remaining 8632 not shown) Histogram of bond angle deviations from ideal: 97.46 - 104.82: 137 104.82 - 112.17: 4261 112.17 - 119.53: 2960 119.53 - 126.89: 4257 126.89 - 134.24: 115 Bond angle restraints: 11730 Sorted by residual: angle pdb=" CA TRP R 178 " pdb=" CB TRP R 178 " pdb=" CG TRP R 178 " ideal model delta sigma weight residual 113.60 123.37 -9.77 1.90e+00 2.77e-01 2.65e+01 angle pdb=" C SER L 95 " pdb=" N SER L 96 " pdb=" CA SER L 96 " ideal model delta sigma weight residual 121.54 112.30 9.24 1.91e+00 2.74e-01 2.34e+01 angle pdb=" C TYR H 104 " pdb=" N GLN H 105 " pdb=" CA GLN H 105 " ideal model delta sigma weight residual 121.54 130.40 -8.86 1.91e+00 2.74e-01 2.15e+01 angle pdb=" CA TYR N 32 " pdb=" CB TYR N 32 " pdb=" CG TYR N 32 " ideal model delta sigma weight residual 113.90 122.23 -8.33 1.80e+00 3.09e-01 2.14e+01 angle pdb=" C THR N 34 " pdb=" CA THR N 34 " pdb=" CB THR N 34 " ideal model delta sigma weight residual 109.34 103.07 6.27 1.55e+00 4.16e-01 1.63e+01 ... (remaining 11725 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.41: 4772 22.41 - 44.82: 247 44.82 - 67.22: 23 67.22 - 89.63: 7 89.63 - 112.04: 2 Dihedral angle restraints: 5051 sinusoidal: 1888 harmonic: 3163 Sorted by residual: dihedral pdb=" CA THR N 34 " pdb=" C THR N 34 " pdb=" N LEU N 35 " pdb=" CA LEU N 35 " ideal model delta harmonic sigma weight residual 180.00 -143.57 -36.43 0 5.00e+00 4.00e-02 5.31e+01 dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual 93.00 152.59 -59.59 1 1.00e+01 1.00e-02 4.74e+01 dihedral pdb=" CA LEU N 35 " pdb=" C LEU N 35 " pdb=" N GLY N 36 " pdb=" CA GLY N 36 " ideal model delta harmonic sigma weight residual 180.00 154.00 26.00 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 5048 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 915 0.056 - 0.113: 315 0.113 - 0.169: 74 0.169 - 0.226: 10 0.226 - 0.282: 3 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CB THR N 34 " pdb=" CA THR N 34 " pdb=" OG1 THR N 34 " pdb=" CG2 THR N 34 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.99e+00 chirality pdb=" CA HIS H 110 " pdb=" N HIS H 110 " pdb=" C HIS H 110 " pdb=" CB HIS H 110 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA PHE R 519 " pdb=" N PHE R 519 " pdb=" C PHE R 519 " pdb=" CB PHE R 519 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 1314 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA R 214 " -0.073 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO R 215 " 0.187 5.00e-02 4.00e+02 pdb=" CA PRO R 215 " -0.056 5.00e-02 4.00e+02 pdb=" CD PRO R 215 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 526 " -0.033 2.00e-02 2.50e+03 2.70e-02 1.28e+01 pdb=" CG PHE R 526 " 0.062 2.00e-02 2.50e+03 pdb=" CD1 PHE R 526 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE R 526 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE R 526 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE R 526 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE R 526 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 32 " -0.034 2.00e-02 2.50e+03 2.20e-02 9.70e+00 pdb=" CG TYR N 32 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR N 32 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR N 32 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR N 32 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR N 32 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR N 32 " -0.006 2.00e-02 2.50e+03 pdb=" OH TYR N 32 " -0.001 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 359 2.70 - 3.25: 7901 3.25 - 3.80: 12292 3.80 - 4.35: 15361 4.35 - 4.90: 27163 Nonbonded interactions: 63076 Sorted by model distance: nonbonded pdb=" OD2 ASP N 74 " pdb=" NZ LYS N 77 " model vdw 2.147 2.520 nonbonded pdb=" OD1 ASP K 62 " pdb=" OG1 THR L 111 " model vdw 2.302 2.440 nonbonded pdb=" O THR R 284 " pdb=" OG1 THR R 284 " model vdw 2.313 2.440 nonbonded pdb=" OG SER H 21 " pdb=" O MET H 87 " model vdw 2.314 2.440 nonbonded pdb=" OD2 ASP H 77 " pdb=" NZ LYS H 80 " model vdw 2.315 2.520 ... (remaining 63071 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.010 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.750 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 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 : 0.013 0.105 8637 Z= 0.843 Angle : 1.078 11.918 11730 Z= 0.590 Chirality : 0.060 0.282 1317 Planarity : 0.007 0.108 1478 Dihedral : 13.238 112.041 3023 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.25), residues: 1091 helix: -0.39 (0.26), residues: 370 sheet: 0.20 (0.30), residues: 309 loop : -1.79 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP R 178 HIS 0.009 0.002 HIS H 110 PHE 0.062 0.004 PHE R 526 TYR 0.049 0.004 TYR N 32 ARG 0.011 0.001 ARG L 63 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 163 ASP cc_start: 0.7809 (m-30) cc_final: 0.7579 (m-30) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2253 time to fit residues: 29.4236 Evaluate side-chains 87 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 32 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8637 Z= 0.182 Angle : 0.574 6.004 11730 Z= 0.308 Chirality : 0.043 0.143 1317 Planarity : 0.005 0.071 1478 Dihedral : 5.997 80.203 1216 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.66 % Allowed : 5.61 % Favored : 93.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.01 (0.26), residues: 1091 helix: 0.90 (0.28), residues: 365 sheet: 0.87 (0.30), residues: 310 loop : -1.49 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 178 HIS 0.003 0.001 HIS H 39 PHE 0.018 0.001 PHE R 526 TYR 0.018 0.001 TYR N 32 ARG 0.005 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 102 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8326 (t) cc_final: 0.8101 (m) REVERT: L 190 LYS cc_start: 0.8247 (mmmm) cc_final: 0.7843 (mptt) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.2193 time to fit residues: 31.8780 Evaluate side-chains 95 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 20.0000 chunk 30 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 10.0000 chunk 98 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 78 optimal weight: 0.6980 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 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 0.043 8637 Z= 0.307 Angle : 0.627 7.419 11730 Z= 0.336 Chirality : 0.045 0.155 1317 Planarity : 0.005 0.061 1478 Dihedral : 5.883 81.458 1216 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.87 % Allowed : 8.91 % Favored : 89.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.00 (0.26), residues: 1091 helix: 0.82 (0.28), residues: 367 sheet: 1.00 (0.31), residues: 305 loop : -1.52 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 178 HIS 0.005 0.001 HIS H 110 PHE 0.023 0.002 PHE R 526 TYR 0.034 0.002 TYR N 32 ARG 0.005 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 97 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 75 SER cc_start: 0.8460 (t) cc_final: 0.8194 (m) REVERT: H 104 TYR cc_start: 0.8617 (OUTLIER) cc_final: 0.6256 (t80) REVERT: K 83 MET cc_start: 0.8262 (mmm) cc_final: 0.7906 (tpt) REVERT: L 190 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8109 (mptt) outliers start: 17 outliers final: 13 residues processed: 105 average time/residue: 0.2114 time to fit residues: 30.5096 Evaluate side-chains 109 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 346 VAL Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8637 Z= 0.302 Angle : 0.618 7.642 11730 Z= 0.331 Chirality : 0.045 0.148 1317 Planarity : 0.005 0.060 1478 Dihedral : 5.767 78.751 1216 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 2.20 % Allowed : 10.67 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1091 helix: 0.81 (0.28), residues: 368 sheet: 1.13 (0.31), residues: 303 loop : -1.46 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP R 178 HIS 0.005 0.001 HIS H 110 PHE 0.019 0.002 PHE R 526 TYR 0.030 0.002 TYR N 32 ARG 0.005 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 92 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8472 (t) cc_final: 0.8198 (m) REVERT: H 104 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.6401 (t80) REVERT: H 105 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7320 (tp40) REVERT: K 83 MET cc_start: 0.8167 (mmm) cc_final: 0.7811 (tpt) REVERT: L 190 LYS cc_start: 0.8439 (mmmm) cc_final: 0.8110 (mptt) REVERT: R 118 ASP cc_start: 0.8361 (m-30) cc_final: 0.8111 (m-30) outliers start: 20 outliers final: 16 residues processed: 103 average time/residue: 0.2189 time to fit residues: 30.9382 Evaluate side-chains 107 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 128 ASP Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 538 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 72 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 53 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8637 Z= 0.175 Angle : 0.531 6.090 11730 Z= 0.284 Chirality : 0.042 0.132 1317 Planarity : 0.004 0.051 1478 Dihedral : 5.274 75.503 1216 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.53 % Allowed : 11.44 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.48 (0.27), residues: 1091 helix: 1.32 (0.29), residues: 361 sheet: 1.20 (0.31), residues: 305 loop : -1.28 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.015 0.001 PHE R 176 TYR 0.019 0.001 TYR N 32 ARG 0.007 0.000 ARG R 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 98 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 75 SER cc_start: 0.8356 (t) cc_final: 0.8090 (m) REVERT: H 104 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.6406 (t80) REVERT: H 105 GLN cc_start: 0.7986 (OUTLIER) cc_final: 0.7503 (tp40) outliers start: 23 outliers final: 19 residues processed: 110 average time/residue: 0.2314 time to fit residues: 34.9448 Evaluate side-chains 116 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain K residue 68 PHE Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 538 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 4.9990 chunk 94 optimal weight: 0.8980 chunk 20 optimal weight: 0.0030 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8637 Z= 0.222 Angle : 0.569 8.295 11730 Z= 0.300 Chirality : 0.043 0.138 1317 Planarity : 0.004 0.054 1478 Dihedral : 5.275 74.740 1216 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.64 % Allowed : 12.21 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.47 (0.26), residues: 1091 helix: 1.26 (0.29), residues: 363 sheet: 1.25 (0.31), residues: 305 loop : -1.27 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 178 HIS 0.005 0.001 HIS H 110 PHE 0.015 0.001 PHE R 327 TYR 0.026 0.001 TYR N 32 ARG 0.006 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8439 (t) cc_final: 0.8154 (m) REVERT: H 104 TYR cc_start: 0.8631 (OUTLIER) cc_final: 0.6445 (t80) REVERT: H 105 GLN cc_start: 0.8024 (OUTLIER) cc_final: 0.7385 (tp40) REVERT: R 118 ASP cc_start: 0.8295 (m-30) cc_final: 0.8021 (m-30) outliers start: 24 outliers final: 19 residues processed: 106 average time/residue: 0.2288 time to fit residues: 33.4531 Evaluate side-chains 111 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 538 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.3980 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 76 optimal weight: 0.0980 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 63 optimal weight: 0.0050 chunk 48 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8637 Z= 0.186 Angle : 0.552 8.026 11730 Z= 0.288 Chirality : 0.042 0.132 1317 Planarity : 0.004 0.050 1478 Dihedral : 5.165 72.947 1216 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.53 % Allowed : 12.54 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.60 (0.27), residues: 1091 helix: 1.40 (0.29), residues: 363 sheet: 1.27 (0.31), residues: 312 loop : -1.22 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 178 HIS 0.006 0.001 HIS R 341 PHE 0.021 0.001 PHE K 68 TYR 0.020 0.001 TYR N 32 ARG 0.006 0.000 ARG N 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.996 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8363 (t) cc_final: 0.8092 (m) REVERT: H 104 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.6401 (t80) REVERT: H 105 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7140 (tp40) REVERT: R 118 ASP cc_start: 0.8256 (m-30) cc_final: 0.7987 (m-30) outliers start: 23 outliers final: 19 residues processed: 108 average time/residue: 0.2206 time to fit residues: 32.7640 Evaluate side-chains 116 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 95 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 113 TRP Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 538 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 chunk 31 optimal weight: 20.0000 chunk 20 optimal weight: 0.0980 chunk 66 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8637 Z= 0.146 Angle : 0.515 6.976 11730 Z= 0.270 Chirality : 0.041 0.130 1317 Planarity : 0.004 0.046 1478 Dihedral : 4.875 69.294 1216 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.64 % Allowed : 12.87 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.84 (0.27), residues: 1091 helix: 1.72 (0.30), residues: 354 sheet: 1.35 (0.31), residues: 296 loop : -1.02 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 178 HIS 0.006 0.001 HIS R 341 PHE 0.023 0.001 PHE K 68 TYR 0.015 0.001 TYR N 32 ARG 0.006 0.000 ARG R 386 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 98 time to evaluate : 0.889 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8303 (t) cc_final: 0.8013 (m) REVERT: H 104 TYR cc_start: 0.8608 (OUTLIER) cc_final: 0.6464 (t80) REVERT: H 105 GLN cc_start: 0.7917 (OUTLIER) cc_final: 0.7068 (tp40) REVERT: N 77 LYS cc_start: 0.8344 (pttm) cc_final: 0.8136 (pttm) outliers start: 24 outliers final: 20 residues processed: 112 average time/residue: 0.2146 time to fit residues: 33.0603 Evaluate side-chains 114 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 163 GLU Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 538 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.8980 chunk 63 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN ** L 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8637 Z= 0.183 Angle : 0.535 6.980 11730 Z= 0.280 Chirality : 0.042 0.133 1317 Planarity : 0.004 0.049 1478 Dihedral : 4.851 69.255 1216 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.75 % Allowed : 13.53 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.79 (0.27), residues: 1091 helix: 1.56 (0.29), residues: 364 sheet: 1.37 (0.31), residues: 297 loop : -1.03 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 178 HIS 0.007 0.001 HIS R 341 PHE 0.028 0.001 PHE K 68 TYR 0.021 0.001 TYR N 32 ARG 0.007 0.000 ARG R 386 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 93 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8347 (t) cc_final: 0.8082 (m) REVERT: H 104 TYR cc_start: 0.8637 (OUTLIER) cc_final: 0.6394 (t80) REVERT: H 105 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7154 (tp40) REVERT: N 77 LYS cc_start: 0.8376 (pttm) cc_final: 0.8129 (pttm) REVERT: R 118 ASP cc_start: 0.8232 (m-30) cc_final: 0.7958 (m-30) outliers start: 25 outliers final: 21 residues processed: 109 average time/residue: 0.2221 time to fit residues: 33.2907 Evaluate side-chains 115 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 0.8980 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 68 optimal weight: 0.0060 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8637 Z= 0.150 Angle : 0.515 6.865 11730 Z= 0.269 Chirality : 0.041 0.128 1317 Planarity : 0.004 0.047 1478 Dihedral : 4.710 67.475 1216 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.31 % Allowed : 14.08 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.95 (0.27), residues: 1091 helix: 1.79 (0.30), residues: 355 sheet: 1.45 (0.31), residues: 296 loop : -0.96 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 178 HIS 0.007 0.001 HIS R 341 PHE 0.020 0.001 PHE R 176 TYR 0.017 0.001 TYR N 32 ARG 0.007 0.000 ARG R 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 94 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8303 (t) cc_final: 0.8033 (m) REVERT: H 104 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.6497 (t80) REVERT: H 105 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.6944 (tp40) outliers start: 21 outliers final: 19 residues processed: 108 average time/residue: 0.2211 time to fit residues: 32.6392 Evaluate side-chains 113 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 92 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 54 TYR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 87 MET Chi-restraints excluded: chain H residue 95 THR Chi-restraints excluded: chain H residue 104 TYR Chi-restraints excluded: chain H residue 105 GLN Chi-restraints excluded: chain H residue 188 VAL Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 182 THR Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 233 VAL Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 538 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 23 optimal weight: 0.4980 chunk 85 optimal weight: 0.2980 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.192287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.139274 restraints weight = 10038.249| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.75 r_work: 0.3241 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8637 Z= 0.188 Angle : 0.538 6.788 11730 Z= 0.281 Chirality : 0.042 0.133 1317 Planarity : 0.004 0.050 1478 Dihedral : 4.821 68.141 1216 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.64 % Allowed : 13.97 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.52 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.85 (0.27), residues: 1091 helix: 1.58 (0.29), residues: 363 sheet: 1.42 (0.31), residues: 297 loop : -0.97 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 178 HIS 0.007 0.001 HIS R 341 PHE 0.021 0.001 PHE R 176 TYR 0.022 0.001 TYR N 32 ARG 0.008 0.000 ARG R 386 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2025.69 seconds wall clock time: 37 minutes 13.22 seconds (2233.22 seconds total)