Starting phenix.real_space_refine on Fri Jul 19 16:19:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/07_2024/8kae_37008.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/07_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_37008/07_2024/8kae_37008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/07_2024/8kae_37008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/07_2024/8kae_37008.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kae_37008/07_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-5388/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: 4.80, per 1000 atoms: 0.57 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: 2.90 Conformation dependent library (CDL) restraints added in 1.6 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: 0.96 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: 3.06 Time building geometry restraints manager: 3.21 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 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 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 ========== 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: 1.230 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.610 Find NCS groups from input model: 0.100 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- 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 : 0.878 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: 0.2392 time to fit residues: 31.4572 Evaluate side-chains 87 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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: 0.8980 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 84 optimal weight: 0.9980 chunk 32 optimal weight: 8.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.7636 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8637 Z= 0.186 Angle : 0.575 5.935 11730 Z= 0.308 Chirality : 0.043 0.143 1317 Planarity : 0.005 0.072 1478 Dihedral : 6.828 90.906 1218 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.77 % Allowed : 6.27 % Favored : 92.96 % 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: -0.05 (0.26), residues: 1091 helix: 0.97 (0.28), residues: 372 sheet: 0.77 (0.31), residues: 290 loop : -1.51 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.017 0.001 PHE R 526 TYR 0.018 0.001 TYR N 32 ARG 0.004 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: 7 poor density : 101 time to evaluate : 0.934 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8327 (t) cc_final: 0.8103 (m) REVERT: L 190 LYS cc_start: 0.8372 (mmmm) cc_final: 0.8012 (mptt) REVERT: N 91 ASP cc_start: 0.8410 (m-30) cc_final: 0.7725 (m-30) outliers start: 7 outliers final: 4 residues processed: 104 average time/residue: 0.2054 time to fit residues: 29.6540 Evaluate side-chains 98 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 94 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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 128 ASP 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: 6.9990 chunk 30 optimal weight: 20.0000 chunk 81 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 87 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 33 optimal weight: 20.0000 chunk 78 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7667 moved from start: 0.1626 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= 0.215 Angle : 0.577 7.119 11730 Z= 0.306 Chirality : 0.043 0.144 1317 Planarity : 0.004 0.061 1478 Dihedral : 6.355 84.620 1218 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.76 % Allowed : 8.69 % Favored : 89.55 % 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: 0.23 (0.26), residues: 1091 helix: 1.18 (0.29), residues: 374 sheet: 1.16 (0.32), residues: 278 loop : -1.49 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 178 HIS 0.003 0.001 HIS H 110 PHE 0.017 0.001 PHE R 526 TYR 0.027 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 112 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 75 SER cc_start: 0.8425 (t) cc_final: 0.8183 (m) REVERT: H 104 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.6182 (t80) REVERT: K 83 MET cc_start: 0.8324 (mmm) cc_final: 0.7822 (tpt) REVERT: N 91 ASP cc_start: 0.8438 (m-30) cc_final: 0.7745 (m-30) REVERT: R 362 ASP cc_start: 0.6903 (OUTLIER) cc_final: 0.6432 (t0) REVERT: R 537 VAL cc_start: 0.7238 (OUTLIER) cc_final: 0.7003 (t) outliers start: 16 outliers final: 11 residues processed: 103 average time/residue: 0.2162 time to fit residues: 30.5062 Evaluate side-chains 107 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.830 ------------------------------------------------------------------------------- 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 L residue 72 ASP 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 362 ASP Chi-restraints excluded: chain R residue 423 VAL Chi-restraints excluded: chain R residue 537 VAL Chi-restraints excluded: chain R residue 538 ASN 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: 6.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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: 0.7767 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 8637 Z= 0.461 Angle : 0.713 9.049 11730 Z= 0.379 Chirality : 0.048 0.172 1317 Planarity : 0.005 0.061 1478 Dihedral : 6.530 85.238 1218 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.31 % Allowed : 11.00 % Favored : 86.69 % 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: -0.10 (0.26), residues: 1091 helix: 0.77 (0.28), residues: 373 sheet: 0.90 (0.31), residues: 301 loop : -1.58 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP R 178 HIS 0.008 0.002 HIS H 110 PHE 0.026 0.002 PHE R 526 TYR 0.036 0.002 TYR N 32 ARG 0.006 0.001 ARG R 386 *********************** 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 110 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 104 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.6478 (t80) REVERT: H 105 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.7396 (tp40) REVERT: K 83 MET cc_start: 0.8046 (mmm) cc_final: 0.7819 (tpp) REVERT: L 190 LYS cc_start: 0.8442 (mmmm) cc_final: 0.8112 (mptt) REVERT: R 361 LYS cc_start: 0.7773 (pttm) cc_final: 0.7408 (ttpt) REVERT: R 362 ASP cc_start: 0.7253 (OUTLIER) cc_final: 0.6605 (t0) outliers start: 21 outliers final: 14 residues processed: 102 average time/residue: 0.2216 time to fit residues: 31.1549 Evaluate side-chains 103 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 86 time to evaluate : 0.936 ------------------------------------------------------------------------------- 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 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 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 362 ASP 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: 0.9990 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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: 0.7655 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8637 Z= 0.190 Angle : 0.550 6.387 11730 Z= 0.292 Chirality : 0.042 0.136 1317 Planarity : 0.004 0.055 1478 Dihedral : 6.058 75.679 1218 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.64 % Allowed : 11.77 % Favored : 85.59 % 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: 0.33 (0.26), residues: 1091 helix: 1.32 (0.29), residues: 368 sheet: 1.18 (0.32), residues: 274 loop : -1.38 (0.28), residues: 449 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 0.015 0.001 PHE R 176 TYR 0.021 0.001 TYR R 160 ARG 0.005 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 116 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 92 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 75 SER cc_start: 0.8350 (t) cc_final: 0.8121 (m) REVERT: H 104 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.6275 (t80) REVERT: H 105 GLN cc_start: 0.8000 (OUTLIER) cc_final: 0.7367 (tp40) REVERT: K 83 MET cc_start: 0.8213 (mmm) cc_final: 0.7924 (tpp) REVERT: N 91 ASP cc_start: 0.8410 (m-30) cc_final: 0.7710 (m-30) REVERT: R 362 ASP cc_start: 0.7014 (OUTLIER) cc_final: 0.6436 (t0) outliers start: 24 outliers final: 17 residues processed: 106 average time/residue: 0.2129 time to fit residues: 31.0385 Evaluate side-chains 108 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 88 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 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 R residue 110 LEU Chi-restraints excluded: chain R residue 128 ASP 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 362 ASP 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: 9.9990 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7686 moved from start: 0.1831 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= 0.241 Angle : 0.573 7.024 11730 Z= 0.303 Chirality : 0.043 0.142 1317 Planarity : 0.004 0.053 1478 Dihedral : 5.817 66.111 1218 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.86 % Allowed : 12.21 % 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: 0.52 (0.27), residues: 1091 helix: 1.38 (0.29), residues: 362 sheet: 1.28 (0.31), residues: 291 loop : -1.24 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 178 HIS 0.005 0.001 HIS H 110 PHE 0.015 0.001 PHE R 176 TYR 0.028 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 117 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 91 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 75 SER cc_start: 0.8397 (t) cc_final: 0.8149 (m) REVERT: H 104 TYR cc_start: 0.8667 (OUTLIER) cc_final: 0.6334 (t80) REVERT: H 105 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7533 (tp40) REVERT: K 83 MET cc_start: 0.8212 (mmm) cc_final: 0.7975 (tpp) REVERT: N 91 ASP cc_start: 0.8421 (m-30) cc_final: 0.7724 (m-30) REVERT: R 362 ASP cc_start: 0.7072 (OUTLIER) cc_final: 0.6491 (t0) outliers start: 26 outliers final: 19 residues processed: 105 average time/residue: 0.2105 time to fit residues: 30.4071 Evaluate side-chains 110 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 88 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 R residue 110 LEU Chi-restraints excluded: chain R residue 128 ASP 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 345 VAL Chi-restraints excluded: chain R residue 362 ASP 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: 0.7980 chunk 11 optimal weight: 1.9990 chunk 59 optimal weight: 0.3980 chunk 76 optimal weight: 0.1980 chunk 87 optimal weight: 0.8980 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 0.0470 chunk 63 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.4278 ------------------------------------------------------------------------------- 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: 0.7571 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8637 Z= 0.137 Angle : 0.500 6.650 11730 Z= 0.263 Chirality : 0.041 0.128 1317 Planarity : 0.004 0.050 1478 Dihedral : 4.682 51.363 1218 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.98 % Allowed : 12.98 % Favored : 85.04 % 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: 0.96 (0.27), residues: 1091 helix: 1.91 (0.30), residues: 355 sheet: 1.38 (0.32), residues: 282 loop : -0.93 (0.30), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 178 HIS 0.002 0.001 HIS H 110 PHE 0.014 0.001 PHE R 176 TYR 0.022 0.001 TYR R 160 ARG 0.005 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: 18 poor density : 100 time to evaluate : 0.869 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8208 (t) cc_final: 0.7924 (m) REVERT: H 104 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.6413 (t80) REVERT: H 105 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.6942 (tp40) REVERT: K 83 MET cc_start: 0.8267 (mmm) cc_final: 0.8017 (tpp) REVERT: L 211 PHE cc_start: 0.6843 (t80) cc_final: 0.6510 (t80) REVERT: N 77 LYS cc_start: 0.8402 (pttm) cc_final: 0.8195 (pttm) REVERT: N 91 ASP cc_start: 0.8421 (m-30) cc_final: 0.7749 (m-30) REVERT: R 362 ASP cc_start: 0.6594 (OUTLIER) cc_final: 0.5955 (t0) outliers start: 18 outliers final: 12 residues processed: 109 average time/residue: 0.2119 time to fit residues: 31.8902 Evaluate side-chains 109 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 94 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain L residue 119 ILE Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 199 THR Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 362 ASP Chi-restraints excluded: chain R residue 423 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.4980 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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: 0.7658 moved from start: 0.2199 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= 0.222 Angle : 0.558 7.081 11730 Z= 0.293 Chirality : 0.042 0.137 1317 Planarity : 0.004 0.050 1478 Dihedral : 4.673 39.652 1218 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.53 % Allowed : 13.53 % Favored : 83.94 % 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: 0.90 (0.27), residues: 1091 helix: 1.76 (0.30), residues: 356 sheet: 1.31 (0.31), residues: 303 loop : -0.94 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 178 HIS 0.004 0.001 HIS H 110 PHE 0.020 0.001 PHE R 176 TYR 0.026 0.001 TYR N 32 ARG 0.007 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 115 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.894 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8261 (t) cc_final: 0.8004 (m) REVERT: H 104 TYR cc_start: 0.8688 (OUTLIER) cc_final: 0.6324 (t80) REVERT: H 105 GLN cc_start: 0.7974 (OUTLIER) cc_final: 0.7262 (tp40) REVERT: K 83 MET cc_start: 0.8273 (mmm) cc_final: 0.8008 (tpp) REVERT: L 211 PHE cc_start: 0.6825 (t80) cc_final: 0.6505 (t80) REVERT: N 91 ASP cc_start: 0.8448 (m-30) cc_final: 0.7751 (m-30) REVERT: R 118 ASP cc_start: 0.7767 (m-30) cc_final: 0.7276 (m-30) REVERT: R 362 ASP cc_start: 0.6755 (OUTLIER) cc_final: 0.6184 (t0) outliers start: 23 outliers final: 19 residues processed: 107 average time/residue: 0.2112 time to fit residues: 31.1005 Evaluate side-chains 114 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 148 VAL Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 128 ASP 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 362 ASP 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: 0.8980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 76 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 63 optimal weight: 0.0040 overall best weight: 0.8994 ------------------------------------------------------------------------------- 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: 0.7638 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8637 Z= 0.187 Angle : 0.541 7.057 11730 Z= 0.284 Chirality : 0.042 0.132 1317 Planarity : 0.004 0.049 1478 Dihedral : 4.550 31.850 1218 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.42 % Allowed : 13.75 % Favored : 83.83 % 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: 0.96 (0.27), residues: 1091 helix: 1.81 (0.30), residues: 356 sheet: 1.39 (0.32), residues: 288 loop : -0.88 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP K 36 HIS 0.003 0.001 HIS H 110 PHE 0.021 0.001 PHE R 176 TYR 0.022 0.001 TYR R 160 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 114 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8213 (t) cc_final: 0.7968 (m) REVERT: H 104 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.6411 (t80) REVERT: H 105 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7098 (tp40) REVERT: K 83 MET cc_start: 0.8274 (mmm) cc_final: 0.8011 (tpp) REVERT: N 91 ASP cc_start: 0.8436 (m-30) cc_final: 0.7764 (m-30) REVERT: R 362 ASP cc_start: 0.6722 (OUTLIER) cc_final: 0.6154 (t0) outliers start: 22 outliers final: 19 residues processed: 104 average time/residue: 0.2198 time to fit residues: 31.3918 Evaluate side-chains 114 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.890 ------------------------------------------------------------------------------- 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 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 117 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 128 ASP 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 345 VAL Chi-restraints excluded: chain R residue 362 ASP 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: 0.0970 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 85 optimal weight: 0.0070 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 7.9990 chunk 68 optimal weight: 0.4980 overall best weight: 0.4196 ------------------------------------------------------------------------------- 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: 0.7562 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8637 Z= 0.134 Angle : 0.502 7.017 11730 Z= 0.262 Chirality : 0.041 0.129 1317 Planarity : 0.004 0.048 1478 Dihedral : 4.241 31.033 1218 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.09 % Allowed : 14.19 % 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: 1.17 (0.27), residues: 1091 helix: 2.07 (0.30), residues: 354 sheet: 1.44 (0.32), residues: 283 loop : -0.74 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP R 178 HIS 0.002 0.001 HIS H 219 PHE 0.019 0.001 PHE R 176 TYR 0.021 0.001 TYR R 160 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: 19 poor density : 96 time to evaluate : 0.832 Fit side-chains revert: symmetry clash REVERT: H 75 SER cc_start: 0.8202 (t) cc_final: 0.7937 (m) REVERT: H 104 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.6248 (t80) REVERT: H 105 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7078 (tp40) REVERT: L 211 PHE cc_start: 0.7125 (t80) cc_final: 0.6804 (t80) REVERT: N 91 ASP cc_start: 0.8395 (m-30) cc_final: 0.7629 (m-30) REVERT: R 362 ASP cc_start: 0.6549 (OUTLIER) cc_final: 0.5888 (t0) outliers start: 19 outliers final: 15 residues processed: 107 average time/residue: 0.2058 time to fit residues: 30.4503 Evaluate side-chains 112 residues out of total 909 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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 117 VAL Chi-restraints excluded: chain L residue 148 VAL Chi-restraints excluded: chain L residue 196 CYS Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 198 LEU Chi-restraints excluded: chain R residue 213 ILE Chi-restraints excluded: chain R residue 362 ASP 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: 1.9990 chunk 26 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 30.0000 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 15 optimal weight: 10.0000 chunk 75 optimal weight: 4.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.189902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136388 restraints weight = 10099.718| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.60 r_work: 0.3213 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2460 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= 0.187 Angle : 0.540 6.859 11730 Z= 0.281 Chirality : 0.042 0.131 1317 Planarity : 0.004 0.049 1478 Dihedral : 4.294 31.469 1218 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.31 % Allowed : 14.19 % Favored : 83.50 % 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: 1.07 (0.27), residues: 1091 helix: 1.89 (0.30), residues: 357 sheet: 1.47 (0.32), residues: 283 loop : -0.79 (0.30), residues: 451 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 0.023 0.001 PHE K 47 TYR 0.022 0.001 TYR R 160 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: 1943.63 seconds wall clock time: 35 minutes 24.07 seconds (2124.07 seconds total)