Starting phenix.real_space_refine on Sat Aug 3 15:48:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/08_2024/8kae_37008.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/08_2024/8kae_37008.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/08_2024/8kae_37008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/08_2024/8kae_37008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/08_2024/8kae_37008.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/08_2024/8kae_37008.cif" } 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-5409/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: 4.91, per 1000 atoms: 0.58 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: 2.95 Conformation dependent library (CDL) restraints added in 1.7 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... Secondary structure from input PDB file: 31 helices and 16 sheets defined 37.1% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'H' and resid 32 through 36 removed outlier: 3.841A pdb=" N TYR H 36 " --> pdb=" O PHE H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 95 removed outlier: 3.569A pdb=" N ASP H 94 " --> pdb=" O ARG H 91 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR H 95 " --> pdb=" O ALA H 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 91 through 95' Processing helix chain 'H' and resid 175 through 177 No H-bonds generated for 'chain 'H' and resid 175 through 177' Processing helix chain 'H' and resid 206 through 211 removed outlier: 4.211A pdb=" N THR H 210 " --> pdb=" O SER H 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 123 through 130 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 189 Processing helix chain 'N' and resid 88 through 92 removed outlier: 3.793A pdb=" N THR N 92 " --> pdb=" O PRO N 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 118 Processing helix chain 'R' and resid 122 through 124 No H-bonds generated for 'chain 'R' and resid 122 through 124' Processing helix chain 'R' and resid 125 through 134 removed outlier: 3.575A pdb=" N GLN R 130 " --> pdb=" O LEU R 126 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN R 131 " --> pdb=" O LEU R 127 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 165 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) removed outlier: 4.322A pdb=" N ASP R 163 " --> pdb=" O GLY R 159 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ARG R 164 " --> pdb=" O TYR R 160 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE R 165 " --> pdb=" O LEU R 161 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 185 Processing helix chain 'R' and resid 186 through 188 No H-bonds generated for 'chain 'R' and resid 186 through 188' Processing helix chain 'R' and resid 193 through 220 removed outlier: 3.557A pdb=" N VAL R 197 " --> pdb=" O PHE R 193 " (cutoff:3.500A) Proline residue: R 215 - end of helix Processing helix chain 'R' and resid 226 through 236 Processing helix chain 'R' and resid 237 through 257 removed outlier: 3.627A pdb=" N GLY R 241 " --> pdb=" O ALA R 237 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N TYR R 246 " --> pdb=" O SER R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 264 removed outlier: 3.625A pdb=" N ARG R 264 " --> pdb=" O TRP R 261 " (cutoff:3.500A) Processing helix chain 'R' and resid 265 through 277 removed outlier: 4.221A pdb=" N LEU R 269 " --> pdb=" O VAL R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 302 through 310 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) Processing helix chain 'R' and resid 312 through 347 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 362 through 389 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) Processing helix chain 'R' and resid 394 through 412 removed outlier: 3.791A pdb=" N LEU R 398 " --> pdb=" O ARG R 394 " (cutoff:3.500A) Processing helix chain 'R' and resid 413 through 418 Processing helix chain 'R' and resid 422 through 438 removed outlier: 3.886A pdb=" N PHE R 437 " --> pdb=" O GLU R 433 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N SER R 438 " --> pdb=" O THR R 434 " (cutoff:3.500A) Processing helix chain 'R' and resid 442 through 448 Processing helix chain 'R' and resid 456 through 470 Processing helix chain 'R' and resid 474 through 488 removed outlier: 3.615A pdb=" N LEU R 478 " --> pdb=" O GLY R 474 " (cutoff:3.500A) Processing helix chain 'R' and resid 493 through 505 Processing helix chain 'R' and resid 506 through 541 removed outlier: 4.221A pdb=" N PHE R 510 " --> pdb=" O MET R 506 " (cutoff:3.500A) 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) removed outlier: 4.310A pdb=" N ALA R 541 " --> pdb=" O VAL R 537 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 7 through 11 Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 16 removed outlier: 6.130A pdb=" N GLY H 14 " --> pdb=" O THR H 129 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE H 38 " --> pdb=" O TYR H 54 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N TYR H 54 " --> pdb=" O ILE H 38 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TRP H 40 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AA3, 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=AA4, 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=AA5, first strand: chain 'H' and resid 169 through 173 Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AA7, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.577A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 10 through 12 removed outlier: 6.577A pdb=" N GLY K 10 " --> pdb=" O THR K 118 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR K 110 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 7 through 9 Processing sheet with id=AB1, first strand: chain 'L' and resid 12 through 14 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=AB2, first strand: chain 'L' and resid 12 through 14 Processing sheet with id=AB3, 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=AB4, first strand: chain 'L' and resid 155 through 156 Processing sheet with id=AB5, first strand: chain 'N' and resid 5 through 7 Processing sheet with id=AB6, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.147A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.147A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) 473 hydrogen bonds defined for protein. 1281 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: 2.82 Time building geometry restraints manager: 3.26 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 1.367 1.440 -0.073 2.00e-02 2.50e+03 1.32e+01 bond pdb=" C07 YUX R 601 " pdb=" C08 YUX R 601 " ideal model delta sigma weight residual 1.460 1.520 -0.060 2.00e-02 2.50e+03 9.14e+00 bond pdb=" C04 YUX R 601 " pdb=" C05 YUX R 601 " ideal model delta sigma weight residual 1.481 1.536 -0.055 2.00e-02 2.50e+03 7.61e+00 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=" C07 YUX R 601 " pdb=" N24 YUX R 601 " ideal model delta sigma weight residual 1.300 1.354 -0.054 2.00e-02 2.50e+03 7.37e+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 - 26.56: 4875 26.56 - 53.13: 162 53.13 - 79.69: 11 79.69 - 106.26: 2 106.26 - 132.82: 3 Dihedral angle restraints: 5053 sinusoidal: 1890 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 5050 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: 358 2.70 - 3.25: 7885 3.25 - 3.80: 12282 3.80 - 4.35: 15294 4.35 - 4.90: 27145 Nonbonded interactions: 62964 Sorted by model distance: nonbonded pdb=" OD2 ASP N 74 " pdb=" NZ LYS N 77 " model vdw 2.147 3.120 nonbonded pdb=" OD1 ASP K 62 " pdb=" OG1 THR L 111 " model vdw 2.302 3.040 nonbonded pdb=" O THR R 284 " pdb=" OG1 THR R 284 " model vdw 2.313 3.040 nonbonded pdb=" OG SER H 21 " pdb=" O MET H 87 " model vdw 2.314 3.040 nonbonded pdb=" OD2 ASP H 77 " pdb=" NZ LYS H 80 " model vdw 2.315 3.120 ... (remaining 62959 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.810 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.480 ------------------------------------------------------------------------------- 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= 0.849 Angle : 1.058 11.918 11730 Z= 0.585 Chirality : 0.060 0.282 1317 Planarity : 0.007 0.108 1478 Dihedral : 13.537 132.821 3025 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 : 0.928 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: 0.2469 time to fit residues: 32.2355 Evaluate side-chains 87 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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: 0.7980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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: 0.7622 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8637 Z= 0.168 Angle : 0.573 5.986 11730 Z= 0.307 Chirality : 0.043 0.140 1317 Planarity : 0.005 0.071 1478 Dihedral : 6.828 90.659 1218 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.66 % Allowed : 6.27 % Favored : 93.07 % 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: 1.00 (0.28), residues: 372 sheet: 0.74 (0.31), residues: 301 loop : -1.51 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 178 HIS 0.003 0.001 HIS H 219 PHE 0.016 0.001 PHE R 526 TYR 0.017 0.001 TYR R 160 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 109 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8293 (t) cc_final: 0.8049 (m) REVERT: L 8 GLN cc_start: 0.7066 (mt0) cc_final: 0.6811 (mt0) REVERT: L 190 LYS cc_start: 0.8410 (mmmm) cc_final: 0.8049 (mmtm) REVERT: N 91 ASP cc_start: 0.8468 (m-30) cc_final: 0.7793 (m-30) outliers start: 6 outliers final: 3 residues processed: 105 average time/residue: 0.2084 time to fit residues: 30.3033 Evaluate side-chains 95 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 92 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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: 30.0000 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 78 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.7633 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8637 Z= 0.176 Angle : 0.558 7.258 11730 Z= 0.295 Chirality : 0.042 0.137 1317 Planarity : 0.004 0.060 1478 Dihedral : 6.246 81.612 1218 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.10 % Allowed : 9.02 % Favored : 89.88 % 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: 0.42 (0.26), residues: 1091 helix: 1.36 (0.29), residues: 372 sheet: 1.16 (0.32), residues: 285 loop : -1.34 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 178 HIS 0.002 0.001 HIS H 110 PHE 0.016 0.001 PHE K 68 TYR 0.022 0.001 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 110 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 100 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 21 SER cc_start: 0.8302 (t) cc_final: 0.8021 (t) REVERT: H 75 SER cc_start: 0.8331 (t) cc_final: 0.8081 (m) REVERT: H 104 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.6149 (t80) REVERT: L 190 LYS cc_start: 0.8484 (mmmm) cc_final: 0.8123 (mmtm) REVERT: N 91 ASP cc_start: 0.8447 (m-30) cc_final: 0.7726 (m-30) REVERT: R 192 TYR cc_start: 0.8131 (m-80) cc_final: 0.7890 (m-80) outliers start: 10 outliers final: 7 residues processed: 104 average time/residue: 0.2184 time to fit residues: 31.0242 Evaluate side-chains 103 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 95 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 GLN 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 L residue 6 MET Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 212 THR 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: 4.9990 chunk 73 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 20.0000 chunk 65 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 93 optimal weight: 0.0470 chunk 28 optimal weight: 20.0000 overall best weight: 1.9284 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8637 Z= 0.329 Angle : 0.639 7.785 11730 Z= 0.339 Chirality : 0.045 0.156 1317 Planarity : 0.005 0.058 1478 Dihedral : 6.273 78.723 1218 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.09 % Allowed : 10.01 % Favored : 87.90 % 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: 0.26 (0.26), residues: 1091 helix: 1.17 (0.28), residues: 368 sheet: 1.09 (0.31), residues: 298 loop : -1.44 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 178 HIS 0.005 0.001 HIS H 110 PHE 0.022 0.002 PHE R 526 TYR 0.034 0.002 TYR N 32 ARG 0.004 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 114 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: H 21 SER cc_start: 0.8316 (t) cc_final: 0.8037 (t) REVERT: H 75 SER cc_start: 0.8446 (t) cc_final: 0.8162 (m) REVERT: H 104 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.6393 (t80) REVERT: H 105 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7616 (tp40) REVERT: L 190 LYS cc_start: 0.8445 (mmmm) cc_final: 0.8094 (mmtm) REVERT: N 91 ASP cc_start: 0.8427 (m-30) cc_final: 0.7735 (m-30) REVERT: R 192 TYR cc_start: 0.8148 (m-80) cc_final: 0.7863 (m-80) REVERT: R 334 MET cc_start: 0.6824 (ttt) cc_final: 0.6597 (ttt) outliers start: 19 outliers final: 11 residues processed: 107 average time/residue: 0.2066 time to fit residues: 30.5609 Evaluate side-chains 104 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 17 GLN 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 L residue 6 MET 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 345 VAL Chi-restraints excluded: chain R residue 423 VAL 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: 1.9990 chunk 1 optimal weight: 8.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8637 Z= 0.185 Angle : 0.552 6.716 11730 Z= 0.290 Chirality : 0.042 0.140 1317 Planarity : 0.004 0.053 1478 Dihedral : 5.951 67.994 1218 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.87 % Allowed : 10.67 % Favored : 87.46 % 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: 0.61 (0.27), residues: 1091 helix: 1.55 (0.30), residues: 362 sheet: 1.30 (0.32), residues: 276 loop : -1.15 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.016 0.001 PHE R 176 TYR 0.021 0.001 TYR R 160 ARG 0.006 0.000 ARG N 28 *********************** 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 113 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.902 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8343 (t) cc_final: 0.8091 (m) REVERT: H 104 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.6275 (t80) REVERT: H 105 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7188 (tp40) REVERT: K 68 PHE cc_start: 0.6954 (OUTLIER) cc_final: 0.6719 (m-80) REVERT: N 91 ASP cc_start: 0.8422 (m-30) cc_final: 0.7774 (m-30) outliers start: 17 outliers final: 8 residues processed: 107 average time/residue: 0.2291 time to fit residues: 33.8377 Evaluate side-chains 102 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 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 119 ILE Chi-restraints excluded: chain R residue 212 THR Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 10.0000 chunk 94 optimal weight: 0.5980 chunk 20 optimal weight: 0.0370 chunk 61 optimal weight: 0.9990 chunk 25 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 0.0770 chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 overall best weight: 0.7420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8637 Z= 0.169 Angle : 0.530 6.897 11730 Z= 0.278 Chirality : 0.042 0.139 1317 Planarity : 0.004 0.050 1478 Dihedral : 5.006 58.809 1218 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 1.98 % Allowed : 11.11 % Favored : 86.91 % 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: 0.89 (0.27), residues: 1091 helix: 1.84 (0.30), residues: 354 sheet: 1.33 (0.32), residues: 282 loop : -0.94 (0.30), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.014 0.001 PHE R 176 TYR 0.021 0.001 TYR R 160 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 110 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.910 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8342 (t) cc_final: 0.8057 (m) REVERT: H 104 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.6385 (t80) REVERT: H 105 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7140 (tp40) REVERT: N 91 ASP cc_start: 0.8419 (m-30) cc_final: 0.7657 (m-30) outliers start: 18 outliers final: 13 residues processed: 100 average time/residue: 0.2194 time to fit residues: 30.2111 Evaluate side-chains 106 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.901 ------------------------------------------------------------------------------- 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 L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE 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 213 ILE 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: 0.5980 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 64 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.7678 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8637 Z= 0.243 Angle : 0.575 7.003 11730 Z= 0.302 Chirality : 0.043 0.142 1317 Planarity : 0.004 0.050 1478 Dihedral : 4.875 49.141 1218 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.98 % Allowed : 11.66 % Favored : 86.36 % 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: 0.72 (0.27), residues: 1091 helix: 1.51 (0.29), residues: 362 sheet: 1.28 (0.31), residues: 303 loop : -1.06 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 178 HIS 0.005 0.001 HIS H 110 PHE 0.034 0.002 PHE K 68 TYR 0.029 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 109 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 91 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8300 (t) cc_final: 0.8043 (m) REVERT: H 104 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.6490 (t80) REVERT: H 105 GLN cc_start: 0.7998 (OUTLIER) cc_final: 0.7307 (tp40) REVERT: N 91 ASP cc_start: 0.8446 (m-30) cc_final: 0.7779 (m-30) outliers start: 18 outliers final: 15 residues processed: 101 average time/residue: 0.2441 time to fit residues: 33.7140 Evaluate side-chains 104 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE 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 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: 0.5980 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 30.0000 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 chunk 99 optimal weight: 0.4980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8637 Z= 0.243 Angle : 0.574 6.918 11730 Z= 0.302 Chirality : 0.043 0.143 1317 Planarity : 0.004 0.051 1478 Dihedral : 4.719 35.241 1218 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.20 % Allowed : 11.66 % Favored : 86.14 % 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: 0.69 (0.27), residues: 1091 helix: 1.46 (0.29), residues: 362 sheet: 1.29 (0.31), residues: 303 loop : -1.07 (0.30), residues: 426 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 0.026 0.002 PHE K 68 TYR 0.026 0.001 TYR N 32 ARG 0.006 0.000 ARG N 28 *********************** 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 108 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 1.136 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8332 (t) cc_final: 0.8072 (m) REVERT: H 104 TYR cc_start: 0.8671 (OUTLIER) cc_final: 0.6464 (t80) REVERT: H 105 GLN cc_start: 0.8021 (OUTLIER) cc_final: 0.7356 (tp40) REVERT: N 91 ASP cc_start: 0.8442 (m-30) cc_final: 0.7781 (m-30) outliers start: 20 outliers final: 15 residues processed: 99 average time/residue: 0.2297 time to fit residues: 31.2662 Evaluate side-chains 105 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 108 GLN Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE 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 212 THR Chi-restraints excluded: chain R residue 213 ILE 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: 4.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8637 Z= 0.259 Angle : 0.588 7.105 11730 Z= 0.309 Chirality : 0.044 0.155 1317 Planarity : 0.004 0.051 1478 Dihedral : 4.713 32.690 1218 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 2.20 % Allowed : 11.66 % Favored : 86.14 % 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: 0.65 (0.27), residues: 1091 helix: 1.42 (0.29), residues: 362 sheet: 1.26 (0.31), residues: 293 loop : -1.01 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 178 HIS 0.007 0.001 HIS H 110 PHE 0.022 0.002 PHE R 176 TYR 0.027 0.001 TYR N 32 ARG 0.006 0.000 ARG N 28 *********************** 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 107 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: H 5 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7867 (mm-30) REVERT: H 75 SER cc_start: 0.8322 (t) cc_final: 0.8061 (m) REVERT: H 104 TYR cc_start: 0.8673 (OUTLIER) cc_final: 0.6457 (t80) REVERT: H 105 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7365 (tp40) REVERT: K 83 MET cc_start: 0.7235 (tpp) cc_final: 0.6139 (mmm) REVERT: N 91 ASP cc_start: 0.8447 (m-30) cc_final: 0.7791 (m-30) outliers start: 20 outliers final: 18 residues processed: 99 average time/residue: 0.2199 time to fit residues: 29.7464 Evaluate side-chains 107 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 87 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 108 GLN Chi-restraints excluded: chain H residue 160 LEU Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 198 VAL 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 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: 1.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 68 optimal weight: 0.0770 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8637 Z= 0.226 Angle : 0.570 7.368 11730 Z= 0.300 Chirality : 0.043 0.142 1317 Planarity : 0.004 0.050 1478 Dihedral : 4.631 32.665 1218 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.20 % Allowed : 11.77 % 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: 0.72 (0.27), residues: 1091 helix: 1.49 (0.29), residues: 362 sheet: 1.28 (0.31), residues: 293 loop : -0.98 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP R 178 HIS 0.004 0.001 HIS H 110 PHE 0.022 0.001 PHE R 176 TYR 0.025 0.001 TYR N 32 ARG 0.006 0.000 ARG N 28 ********************** 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 108 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.939 Fit side-chains revert: symmetry clash REVERT: H 5 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7974 (mm-30) REVERT: H 75 SER cc_start: 0.8359 (t) cc_final: 0.8094 (m) REVERT: H 104 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.6448 (t80) REVERT: H 105 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7233 (tp40) REVERT: N 91 ASP cc_start: 0.8443 (m-30) cc_final: 0.7783 (m-30) outliers start: 20 outliers final: 17 residues processed: 100 average time/residue: 0.2438 time to fit residues: 33.6102 Evaluate side-chains 106 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 160 LEU Chi-restraints excluded: chain L residue 6 MET Chi-restraints excluded: chain L residue 50 ILE Chi-restraints excluded: chain L residue 117 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 166 THR Chi-restraints excluded: chain L residue 198 VAL 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 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: 0.9990 chunk 26 optimal weight: 0.7980 chunk 79 optimal weight: 0.2980 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 85 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.188500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.135663 restraints weight = 10033.662| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.69 r_work: 0.3234 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8637 Z= 0.188 Angle : 0.539 7.425 11730 Z= 0.284 Chirality : 0.042 0.139 1317 Planarity : 0.004 0.049 1478 Dihedral : 4.444 32.018 1218 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.87 % Allowed : 11.99 % Favored : 86.14 % 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: 0.88 (0.27), residues: 1091 helix: 1.75 (0.30), residues: 356 sheet: 1.33 (0.32), residues: 278 loop : -0.86 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 178 HIS 0.005 0.001 HIS H 110 PHE 0.021 0.001 PHE R 176 TYR 0.023 0.001 TYR R 160 ARG 0.007 0.000 ARG N 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.64 seconds wall clock time: 34 minutes 34.67 seconds (2074.67 seconds total)