Starting phenix.real_space_refine on Fri Aug 2 21:51:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yi7_39311/08_2024/8yi7_39311_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yi7_39311/08_2024/8yi7_39311.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yi7_39311/08_2024/8yi7_39311.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yi7_39311/08_2024/8yi7_39311.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yi7_39311/08_2024/8yi7_39311_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8yi7_39311/08_2024/8yi7_39311_neut.cif" } resolution = 3.57 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= 0.003 sd= 0.049 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 43 5.16 5 C 3514 2.51 5 N 943 2.21 5 O 1086 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 114": "NH1" <-> "NH2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "A PHE 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A PHE 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 185": "OE1" <-> "OE2" Residue "A TYR 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "B TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 56": "OD1" <-> "OD2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B ASP 84": "OD1" <-> "OD2" Residue "B GLU 95": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B ASP 115": "OD1" <-> "OD2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B TYR 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 188": "OE1" <-> "OE2" Residue "B ASP 196": "OD1" <-> "OD2" Residue "B GLU 221": "OE1" <-> "OE2" Residue "B TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 228": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 301": "NH1" <-> "NH2" Residue "B ASP 312": "OD1" <-> "OD2" Residue "B ARG 313": "NH1" <-> "NH2" Residue "C ARG 65": "NH1" <-> "NH2" Residue "C TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 74": "OD1" <-> "OD2" Residue "C ARG 75": "NH1" <-> "NH2" Residue "C ASP 109": "OD1" <-> "OD2" Residue "C GLU 117": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ASP 38": "OD1" <-> "OD2" Residue "D ASP 40": "OD1" <-> "OD2" Residue "D ARG 51": "NH1" <-> "NH2" Residue "D TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D GLU 128": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 5586 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1485 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 6, 'TRANS': 178} Chain: "B" Number of atoms: 2413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2413 Classifications: {'peptide': 303} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 288} Chain breaks: 1 Chain: "C" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 764 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 94} Chain: "D" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 871 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.02, per 1000 atoms: 0.72 Number of scatterers: 5586 At special positions: 0 Unit cell: (117.41, 97.4064, 101.755, 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 43 16.00 O 1086 8.00 N 943 7.00 C 3514 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 37 " - pdb=" SG CYS A 110 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 85 " - pdb=" SG CYS A 123 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS B 199 " distance=2.25 Simple disulfide: pdb=" SG CYS B 50 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 300 " - pdb=" SG CYS B 327 " distance=2.03 Simple disulfide: pdb=" SG CYS C 28 " - pdb=" SG CYS C 114 " distance=2.02 Simple disulfide: pdb=" SG CYS C 51 " - pdb=" SG CYS C 101 " distance=2.03 Simple disulfide: pdb=" SG CYS C 59 " - pdb=" SG CYS C 105 " distance=2.04 Simple disulfide: pdb=" SG CYS D 29 " - pdb=" SG CYS D 87 " distance=2.03 Simple disulfide: pdb=" SG CYS D 52 " - pdb=" SG CYS D 62 " distance=2.03 Simple disulfide: pdb=" SG CYS D 80 " - pdb=" SG CYS D 86 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " NAG-ASN " NAG C 401 " - " ASN C 48 " " NAG E 1 " - " ASN B 222 " Time building additional restraints: 2.13 Conformation dependent library (CDL) restraints added in 1.3 seconds 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1332 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 13 sheets defined 17.4% alpha, 31.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 35 through 59 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 117 through 147 removed outlier: 4.010A pdb=" N MET A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 Processing helix chain 'A' and resid 187 through 218 removed outlier: 3.937A pdb=" N THR A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 85 Processing helix chain 'B' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE B 23 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 31 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS B 105 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 33 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS B 107 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 35 " --> pdb=" O LYS B 107 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N VAL B 96 " --> pdb=" O LYS B 92 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LYS B 92 " --> pdb=" O VAL B 96 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N HIS B 91 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY B 70 " --> pdb=" O TRP B 60 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 23 through 27 removed outlier: 6.270A pdb=" N ILE B 23 " --> pdb=" O GLU B 34 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N GLU B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N GLU B 25 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL B 32 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS B 27 " --> pdb=" O VAL B 30 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B 31 " --> pdb=" O LEU B 103 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N HIS B 105 " --> pdb=" O TYR B 31 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL B 33 " --> pdb=" O HIS B 105 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS B 107 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LEU B 35 " --> pdb=" O LYS B 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 49 Processing sheet with id=AA4, first strand: chain 'B' and resid 130 through 133 removed outlier: 6.526A pdb=" N GLU B 188 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 152 through 153 Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 160 Processing sheet with id=AA7, first strand: chain 'B' and resid 239 through 245 removed outlier: 5.333A pdb=" N ASN B 240 " --> pdb=" O GLU B 257 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU B 257 " --> pdb=" O ASN B 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 289 through 291 removed outlier: 4.262A pdb=" N ALA B 304 " --> pdb=" O CYS B 327 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N CYS B 327 " --> pdb=" O ALA B 304 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE B 306 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 31 through 34 Processing sheet with id=AB1, first strand: chain 'C' and resid 40 through 42 removed outlier: 5.755A pdb=" N ILE C 41 " --> pdb=" O GLY C 121 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N GLN C 112 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N LEU C 103 " --> pdb=" O GLN C 112 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N CYS C 114 " --> pdb=" O CYS C 101 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY C 95 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU C 68 " --> pdb=" O PHE C 79 " (cutoff:3.500A) removed outlier: 4.766A pdb=" N PHE C 79 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU C 70 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 47 through 56 removed outlier: 4.035A pdb=" N LEU D 50 " --> pdb=" O SER D 63 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N SER D 63 " --> pdb=" O LEU D 50 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N CYS D 52 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLU D 61 " --> pdb=" O CYS D 52 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N ARG D 54 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARG D 59 " --> pdb=" O ARG D 54 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=AB4, first strand: chain 'D' and resid 87 through 88 removed outlier: 3.765A pdb=" N VAL D 111 " --> pdb=" O LEU D 131 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 543 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 2.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1072 1.32 - 1.45: 1396 1.45 - 1.57: 3181 1.57 - 1.69: 0 1.69 - 1.82: 55 Bond restraints: 5704 Sorted by residual: bond pdb=" CA VAL D 107 " pdb=" CB VAL D 107 " ideal model delta sigma weight residual 1.537 1.479 0.058 1.24e-02 6.50e+03 2.20e+01 bond pdb=" CA VAL D 105 " pdb=" CB VAL D 105 " ideal model delta sigma weight residual 1.541 1.488 0.053 1.30e-02 5.92e+03 1.65e+01 bond pdb=" CA PRO B 237 " pdb=" C PRO B 237 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.60e+01 bond pdb=" N VAL B 325 " pdb=" CA VAL B 325 " ideal model delta sigma weight residual 1.457 1.493 -0.035 9.00e-03 1.23e+04 1.54e+01 bond pdb=" N THR B 52 " pdb=" CA THR B 52 " ideal model delta sigma weight residual 1.453 1.489 -0.035 9.20e-03 1.18e+04 1.49e+01 ... (remaining 5699 not shown) Histogram of bond angle deviations from ideal: 99.81 - 106.74: 196 106.74 - 113.68: 3136 113.68 - 120.61: 2602 120.61 - 127.54: 1744 127.54 - 134.47: 43 Bond angle restraints: 7721 Sorted by residual: angle pdb=" N ARG C 65 " pdb=" CA ARG C 65 " pdb=" C ARG C 65 " ideal model delta sigma weight residual 114.62 106.84 7.78 1.14e+00 7.69e-01 4.65e+01 angle pdb=" C THR D 123 " pdb=" CA THR D 123 " pdb=" CB THR D 123 " ideal model delta sigma weight residual 110.78 100.14 10.64 1.60e+00 3.91e-01 4.42e+01 angle pdb=" CA GLY B 72 " pdb=" C GLY B 72 " pdb=" O GLY B 72 " ideal model delta sigma weight residual 122.23 117.93 4.30 6.90e-01 2.10e+00 3.89e+01 angle pdb=" CA THR D 112 " pdb=" C THR D 112 " pdb=" O THR D 112 " ideal model delta sigma weight residual 121.81 115.62 6.19 1.18e+00 7.18e-01 2.75e+01 angle pdb=" N SER D 106 " pdb=" CA SER D 106 " pdb=" C SER D 106 " ideal model delta sigma weight residual 109.59 117.10 -7.51 1.47e+00 4.63e-01 2.61e+01 ... (remaining 7716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.20: 3301 20.20 - 40.40: 196 40.40 - 60.60: 37 60.60 - 80.80: 8 80.80 - 101.00: 6 Dihedral angle restraints: 3548 sinusoidal: 1498 harmonic: 2050 Sorted by residual: dihedral pdb=" CB CYS C 59 " pdb=" SG CYS C 59 " pdb=" SG CYS C 105 " pdb=" CB CYS C 105 " ideal model delta sinusoidal sigma weight residual 93.00 166.24 -73.24 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS B 300 " pdb=" SG CYS B 300 " pdb=" SG CYS B 327 " pdb=" CB CYS B 327 " ideal model delta sinusoidal sigma weight residual -86.00 -147.42 61.42 1 1.00e+01 1.00e-02 5.01e+01 dihedral pdb=" CB CYS B 50 " pdb=" SG CYS B 50 " pdb=" SG CYS B 90 " pdb=" CB CYS B 90 " ideal model delta sinusoidal sigma weight residual 93.00 153.54 -60.54 1 1.00e+01 1.00e-02 4.88e+01 ... (remaining 3545 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 396 0.076 - 0.151: 318 0.151 - 0.227: 119 0.227 - 0.302: 38 0.302 - 0.378: 3 Chirality restraints: 874 Sorted by residual: chirality pdb=" CA THR D 123 " pdb=" N THR D 123 " pdb=" C THR D 123 " pdb=" CB THR D 123 " both_signs ideal model delta sigma weight residual False 2.53 2.90 -0.38 2.00e-01 2.50e+01 3.57e+00 chirality pdb=" CA ASN B 184 " pdb=" N ASN B 184 " pdb=" C ASN B 184 " pdb=" CB ASN B 184 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.32e+00 chirality pdb=" CB VAL B 180 " pdb=" CA VAL B 180 " pdb=" CG1 VAL B 180 " pdb=" CG2 VAL B 180 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 871 not shown) Planarity restraints: 979 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 100 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.22e+00 pdb=" C SER D 100 " 0.053 2.00e-02 2.50e+03 pdb=" O SER D 100 " -0.019 2.00e-02 2.50e+03 pdb=" N ASP D 101 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 196 " -0.014 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C ASP B 196 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP B 196 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 197 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 265 " 0.014 2.00e-02 2.50e+03 2.80e-02 7.83e+00 pdb=" C PRO B 265 " -0.048 2.00e-02 2.50e+03 pdb=" O PRO B 265 " 0.018 2.00e-02 2.50e+03 pdb=" N HIS B 266 " 0.016 2.00e-02 2.50e+03 ... (remaining 976 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 138 2.68 - 3.23: 4878 3.23 - 3.79: 8010 3.79 - 4.34: 11305 4.34 - 4.90: 17923 Nonbonded interactions: 42254 Sorted by model distance: nonbonded pdb=" CD2 LEU B 117 " pdb=" CG2 THR B 146 " model vdw 2.122 3.880 nonbonded pdb=" CG2 THR B 141 " pdb=" OE1 GLU B 192 " model vdw 2.338 3.460 nonbonded pdb=" O ASP A 187 " pdb=" OD1 ASP A 187 " model vdw 2.339 3.040 nonbonded pdb=" NZ LYS B 157 " pdb=" OD2 ASP B 213 " model vdw 2.340 3.120 nonbonded pdb=" O5 NAG C 401 " pdb=" O6 NAG C 401 " model vdw 2.447 2.432 ... (remaining 42249 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 group one per residue 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: 0.740 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 20.040 Find NCS groups from input model: 0.060 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 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 0.058 5704 Z= 0.861 Angle : 1.602 10.638 7721 Z= 1.206 Chirality : 0.114 0.378 874 Planarity : 0.005 0.030 977 Dihedral : 13.654 100.996 2174 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.75 % Allowed : 10.81 % Favored : 87.44 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.32), residues: 687 helix: 3.02 (0.48), residues: 119 sheet: 0.51 (0.35), residues: 230 loop : -0.76 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 60 HIS 0.004 0.001 HIS A 71 PHE 0.026 0.002 PHE D 99 TYR 0.025 0.002 TYR B 268 ARG 0.004 0.001 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 176 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 THR cc_start: 0.8516 (p) cc_final: 0.8123 (p) REVERT: B 114 THR cc_start: 0.8475 (m) cc_final: 0.8270 (p) REVERT: B 271 LEU cc_start: 0.8973 (mt) cc_final: 0.8768 (mt) REVERT: B 275 VAL cc_start: 0.8284 (OUTLIER) cc_final: 0.8017 (m) REVERT: B 276 GLN cc_start: 0.7301 (tt0) cc_final: 0.7020 (pp30) REVERT: D 51 ARG cc_start: 0.8152 (ttm170) cc_final: 0.7787 (ptp-110) REVERT: D 63 SER cc_start: 0.8564 (t) cc_final: 0.8130 (m) REVERT: D 65 GLN cc_start: 0.7776 (tt0) cc_final: 0.7498 (mt0) REVERT: D 96 ARG cc_start: 0.7965 (ptp-170) cc_final: 0.7495 (ptp90) REVERT: D 98 GLN cc_start: 0.8315 (mt0) cc_final: 0.7879 (mt0) outliers start: 11 outliers final: 1 residues processed: 183 average time/residue: 0.1922 time to fit residues: 44.1061 Evaluate side-chains 113 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 57 optimal weight: 0.3980 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 chunk 53 optimal weight: 0.0470 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 39 optimal weight: 0.0670 chunk 61 optimal weight: 4.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 78 GLN B 87 GLN B 99 HIS D 102 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5704 Z= 0.205 Angle : 0.590 7.245 7721 Z= 0.319 Chirality : 0.042 0.157 874 Planarity : 0.004 0.040 977 Dihedral : 7.781 64.229 836 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.38 % Allowed : 16.53 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.32), residues: 687 helix: 3.55 (0.43), residues: 109 sheet: 0.59 (0.35), residues: 226 loop : -0.67 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 118 HIS 0.008 0.001 HIS B 91 PHE 0.012 0.001 PHE A 118 TYR 0.024 0.002 TYR B 314 ARG 0.005 0.001 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6620 (OUTLIER) cc_final: 0.6311 (mp10) REVERT: B 114 THR cc_start: 0.8412 (m) cc_final: 0.8048 (p) REVERT: B 288 ARG cc_start: 0.7309 (ptp-170) cc_final: 0.6772 (mtt180) REVERT: D 51 ARG cc_start: 0.7955 (ttm170) cc_final: 0.7586 (ptp-110) REVERT: D 65 GLN cc_start: 0.8074 (tt0) cc_final: 0.7676 (mp10) REVERT: D 96 ARG cc_start: 0.7762 (ptp-170) cc_final: 0.7498 (ptp-110) REVERT: D 98 GLN cc_start: 0.7947 (mt0) cc_final: 0.7634 (mt0) outliers start: 15 outliers final: 7 residues processed: 114 average time/residue: 0.1846 time to fit residues: 27.2516 Evaluate side-chains 101 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 87 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 97 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 34 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 51 optimal weight: 0.0370 chunk 42 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 39 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 5704 Z= 0.209 Angle : 0.536 6.937 7721 Z= 0.289 Chirality : 0.041 0.191 874 Planarity : 0.004 0.040 977 Dihedral : 5.514 37.686 834 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.50 % Allowed : 18.60 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.32), residues: 687 helix: 3.44 (0.45), residues: 112 sheet: 0.55 (0.34), residues: 232 loop : -0.66 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 60 HIS 0.009 0.001 HIS B 91 PHE 0.013 0.001 PHE B 228 TYR 0.016 0.002 TYR C 71 ARG 0.003 0.000 ARG B 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.663 Fit side-chains REVERT: A 157 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.6309 (mp10) REVERT: B 78 GLN cc_start: 0.7186 (pt0) cc_final: 0.6868 (pt0) REVERT: B 114 THR cc_start: 0.8513 (m) cc_final: 0.8006 (p) REVERT: B 288 ARG cc_start: 0.7466 (ptp-170) cc_final: 0.7195 (mtt180) REVERT: D 51 ARG cc_start: 0.8082 (ttm170) cc_final: 0.7739 (ptp-110) REVERT: D 65 GLN cc_start: 0.8009 (tt0) cc_final: 0.7621 (mt0) REVERT: D 96 ARG cc_start: 0.7713 (ptp-170) cc_final: 0.7407 (ptp90) REVERT: D 98 GLN cc_start: 0.8092 (mt0) cc_final: 0.7822 (mt0) REVERT: D 122 GLN cc_start: 0.6624 (mm-40) cc_final: 0.6315 (mp10) outliers start: 22 outliers final: 9 residues processed: 117 average time/residue: 0.1676 time to fit residues: 25.8350 Evaluate side-chains 104 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 32 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 37 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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: 0.7649 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 5704 Z= 0.174 Angle : 0.513 8.688 7721 Z= 0.272 Chirality : 0.039 0.166 874 Planarity : 0.004 0.040 977 Dihedral : 4.376 26.131 834 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.23 % Allowed : 20.03 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.32), residues: 687 helix: 3.16 (0.46), residues: 109 sheet: 0.71 (0.34), residues: 226 loop : -0.73 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 60 HIS 0.011 0.001 HIS B 91 PHE 0.011 0.001 PHE A 35 TYR 0.013 0.001 TYR C 71 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6581 (OUTLIER) cc_final: 0.6347 (mp10) REVERT: B 78 GLN cc_start: 0.7137 (pt0) cc_final: 0.6808 (pt0) REVERT: B 114 THR cc_start: 0.8258 (m) cc_final: 0.7880 (p) REVERT: B 118 LYS cc_start: 0.8206 (ptmt) cc_final: 0.7945 (ptmt) REVERT: B 288 ARG cc_start: 0.7486 (ptp-170) cc_final: 0.7251 (mtt180) REVERT: D 48 ARG cc_start: 0.6984 (mpt180) cc_final: 0.6367 (mmt180) REVERT: D 51 ARG cc_start: 0.8071 (ttm170) cc_final: 0.7702 (ptp-110) REVERT: D 65 GLN cc_start: 0.8128 (tt0) cc_final: 0.7679 (mt0) REVERT: D 96 ARG cc_start: 0.7689 (ptp-170) cc_final: 0.7431 (ptp90) REVERT: D 98 GLN cc_start: 0.8047 (mt0) cc_final: 0.7815 (mt0) outliers start: 14 outliers final: 8 residues processed: 101 average time/residue: 0.1825 time to fit residues: 24.0243 Evaluate side-chains 101 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 97 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 135 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS B 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5704 Z= 0.277 Angle : 0.564 6.400 7721 Z= 0.299 Chirality : 0.042 0.185 874 Planarity : 0.004 0.037 977 Dihedral : 4.310 17.220 834 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.70 % Allowed : 19.55 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.32), residues: 687 helix: 3.21 (0.47), residues: 112 sheet: 0.64 (0.35), residues: 225 loop : -0.75 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 60 HIS 0.011 0.002 HIS B 91 PHE 0.021 0.002 PHE B 228 TYR 0.014 0.002 TYR B 314 ARG 0.005 0.001 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.667 Fit side-chains REVERT: A 215 TYR cc_start: 0.8991 (t80) cc_final: 0.8730 (t80) REVERT: B 78 GLN cc_start: 0.7221 (pt0) cc_final: 0.6925 (pt0) REVERT: B 114 THR cc_start: 0.8346 (m) cc_final: 0.7957 (p) REVERT: D 51 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7829 (ptp-110) REVERT: D 65 GLN cc_start: 0.8087 (tt0) cc_final: 0.7698 (mt0) REVERT: D 96 ARG cc_start: 0.7718 (ptp-170) cc_final: 0.7461 (ptp90) REVERT: D 98 GLN cc_start: 0.8174 (mt0) cc_final: 0.7869 (mt0) outliers start: 17 outliers final: 10 residues processed: 111 average time/residue: 0.1840 time to fit residues: 26.4329 Evaluate side-chains 102 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 92 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 38 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 65 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 5 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS B 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5704 Z= 0.174 Angle : 0.511 6.462 7721 Z= 0.269 Chirality : 0.039 0.190 874 Planarity : 0.004 0.040 977 Dihedral : 4.133 18.145 834 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.38 % Allowed : 20.99 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.32), residues: 687 helix: 2.89 (0.47), residues: 118 sheet: 0.69 (0.35), residues: 227 loop : -0.76 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 60 HIS 0.012 0.001 HIS B 91 PHE 0.010 0.001 PHE B 140 TYR 0.012 0.001 TYR C 71 ARG 0.004 0.000 ARG B 181 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6483 (mp10) REVERT: B 78 GLN cc_start: 0.7147 (pt0) cc_final: 0.6843 (pt0) REVERT: B 114 THR cc_start: 0.8219 (m) cc_final: 0.7825 (p) REVERT: D 51 ARG cc_start: 0.8063 (ttm170) cc_final: 0.7813 (ptp-110) REVERT: D 65 GLN cc_start: 0.8111 (tt0) cc_final: 0.7705 (mt0) REVERT: D 96 ARG cc_start: 0.7726 (ptp-170) cc_final: 0.7475 (ptp90) REVERT: D 98 GLN cc_start: 0.8108 (mt0) cc_final: 0.7818 (mt0) outliers start: 15 outliers final: 6 residues processed: 101 average time/residue: 0.1852 time to fit residues: 24.1990 Evaluate side-chains 96 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 101 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 48 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 39 optimal weight: 0.0970 chunk 30 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.4617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 5704 Z= 0.169 Angle : 0.503 6.599 7721 Z= 0.265 Chirality : 0.039 0.205 874 Planarity : 0.004 0.043 977 Dihedral : 3.988 17.532 834 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.23 % Allowed : 20.99 % Favored : 76.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.33), residues: 687 helix: 2.89 (0.48), residues: 118 sheet: 0.75 (0.35), residues: 227 loop : -0.81 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 143 HIS 0.012 0.001 HIS B 91 PHE 0.013 0.001 PHE B 140 TYR 0.010 0.001 TYR C 71 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 91 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: B 78 GLN cc_start: 0.7098 (pt0) cc_final: 0.6795 (pt0) REVERT: B 114 THR cc_start: 0.8224 (m) cc_final: 0.7821 (p) REVERT: B 258 TYR cc_start: 0.8517 (m-80) cc_final: 0.8240 (m-80) REVERT: D 48 ARG cc_start: 0.6792 (tpt170) cc_final: 0.6540 (mmt180) REVERT: D 51 ARG cc_start: 0.8108 (ttm170) cc_final: 0.7876 (ptp-110) REVERT: D 65 GLN cc_start: 0.8143 (tt0) cc_final: 0.7699 (mt0) REVERT: D 96 ARG cc_start: 0.7760 (ptp-170) cc_final: 0.7484 (ptp90) REVERT: D 98 GLN cc_start: 0.8111 (mt0) cc_final: 0.7821 (mt0) REVERT: D 128 GLU cc_start: 0.7085 (pp20) cc_final: 0.6197 (pp20) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.1795 time to fit residues: 23.6901 Evaluate side-chains 97 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS B 99 HIS ** C 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 5704 Z= 0.433 Angle : 0.644 6.935 7721 Z= 0.340 Chirality : 0.045 0.274 874 Planarity : 0.004 0.048 977 Dihedral : 4.536 19.714 834 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.54 % Allowed : 21.30 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.32), residues: 687 helix: 2.73 (0.47), residues: 113 sheet: 0.43 (0.34), residues: 229 loop : -1.10 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 144 HIS 0.011 0.002 HIS B 216 PHE 0.029 0.002 PHE B 228 TYR 0.015 0.002 TYR C 71 ARG 0.006 0.001 ARG B 230 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.680 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.6734 (mp10) REVERT: B 78 GLN cc_start: 0.7225 (pt0) cc_final: 0.6935 (pt0) REVERT: D 51 ARG cc_start: 0.8159 (ttm170) cc_final: 0.7890 (ptp-110) REVERT: D 65 GLN cc_start: 0.8162 (tt0) cc_final: 0.7733 (mt0) REVERT: D 96 ARG cc_start: 0.7736 (ptp-170) cc_final: 0.7480 (ptp90) REVERT: D 98 GLN cc_start: 0.8209 (mt0) cc_final: 0.7832 (mt0) REVERT: D 128 GLU cc_start: 0.6980 (pp20) cc_final: 0.6177 (pp20) outliers start: 16 outliers final: 14 residues processed: 104 average time/residue: 0.1848 time to fit residues: 24.9027 Evaluate side-chains 107 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 174 THR Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 26 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.0370 chunk 44 optimal weight: 4.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS C 78 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 5704 Z= 0.203 Angle : 0.541 8.198 7721 Z= 0.282 Chirality : 0.040 0.237 874 Planarity : 0.004 0.051 977 Dihedral : 4.235 17.790 834 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.54 % Allowed : 21.14 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.32), residues: 687 helix: 2.73 (0.47), residues: 118 sheet: 0.50 (0.35), residues: 225 loop : -1.02 (0.32), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 143 HIS 0.011 0.001 HIS B 91 PHE 0.010 0.001 PHE B 228 TYR 0.010 0.001 TYR C 71 ARG 0.003 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 92 time to evaluate : 0.689 Fit side-chains revert: symmetry clash REVERT: A 157 GLN cc_start: 0.6828 (OUTLIER) cc_final: 0.6566 (mp10) REVERT: B 78 GLN cc_start: 0.7194 (pt0) cc_final: 0.6938 (pt0) REVERT: B 258 TYR cc_start: 0.8708 (m-80) cc_final: 0.8444 (m-80) REVERT: C 67 LYS cc_start: 0.7362 (ptmt) cc_final: 0.7097 (ptmt) REVERT: D 48 ARG cc_start: 0.6839 (tpt170) cc_final: 0.6529 (mmt180) REVERT: D 51 ARG cc_start: 0.8171 (ttm170) cc_final: 0.7907 (ptp-110) REVERT: D 65 GLN cc_start: 0.8150 (tt0) cc_final: 0.7658 (mt0) REVERT: D 96 ARG cc_start: 0.7741 (ptp-170) cc_final: 0.7482 (ptp90) REVERT: D 98 GLN cc_start: 0.8233 (mt0) cc_final: 0.7814 (mt0) REVERT: D 128 GLU cc_start: 0.7107 (pp20) cc_final: 0.6307 (pp20) outliers start: 16 outliers final: 11 residues processed: 102 average time/residue: 0.2004 time to fit residues: 26.1496 Evaluate side-chains 102 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 GLN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 67 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 5704 Z= 0.210 Angle : 0.534 8.264 7721 Z= 0.276 Chirality : 0.040 0.232 874 Planarity : 0.004 0.053 977 Dihedral : 4.133 18.179 834 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.07 % Allowed : 21.30 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.32), residues: 687 helix: 2.82 (0.48), residues: 119 sheet: 0.33 (0.35), residues: 233 loop : -0.89 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 256 HIS 0.011 0.001 HIS B 91 PHE 0.014 0.001 PHE B 228 TYR 0.011 0.001 TYR B 314 ARG 0.003 0.000 ARG A 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1374 Ramachandran restraints generated. 687 Oldfield, 0 Emsley, 687 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: B 78 GLN cc_start: 0.7172 (pt0) cc_final: 0.6936 (pt0) REVERT: B 114 THR cc_start: 0.8295 (m) cc_final: 0.7906 (p) REVERT: B 258 TYR cc_start: 0.8676 (m-80) cc_final: 0.8413 (m-80) REVERT: D 48 ARG cc_start: 0.6832 (tpt170) cc_final: 0.6540 (mmt180) REVERT: D 51 ARG cc_start: 0.8145 (ttm170) cc_final: 0.7879 (ptp-110) REVERT: D 65 GLN cc_start: 0.8099 (tt0) cc_final: 0.7606 (mt0) REVERT: D 96 ARG cc_start: 0.7758 (ptp-170) cc_final: 0.7464 (ptp90) REVERT: D 98 GLN cc_start: 0.8244 (mt0) cc_final: 0.7798 (mt0) REVERT: D 128 GLU cc_start: 0.7121 (pp20) cc_final: 0.6335 (pp20) outliers start: 13 outliers final: 11 residues processed: 101 average time/residue: 0.1913 time to fit residues: 24.7651 Evaluate side-chains 102 residues out of total 629 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 91 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 325 VAL Chi-restraints excluded: chain C residue 33 VAL Chi-restraints excluded: chain C residue 34 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 101 ASP Chi-restraints excluded: chain D residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 68 random chunks: chunk 14 optimal weight: 0.0770 chunk 54 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 6 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 39 optimal weight: 0.0040 chunk 61 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.3128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 ASN B 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.156101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.120613 restraints weight = 6825.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.122518 restraints weight = 5457.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.123855 restraints weight = 4799.410| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 5704 Z= 0.162 Angle : 0.514 8.540 7721 Z= 0.267 Chirality : 0.039 0.219 874 Planarity : 0.004 0.052 977 Dihedral : 4.007 18.996 834 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.59 % Allowed : 22.58 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.90 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.32), residues: 687 helix: 2.78 (0.47), residues: 118 sheet: 0.37 (0.35), residues: 233 loop : -0.88 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 143 HIS 0.012 0.001 HIS B 91 PHE 0.012 0.001 PHE B 140 TYR 0.010 0.001 TYR B 314 ARG 0.003 0.000 ARG A 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1637.60 seconds wall clock time: 29 minutes 37.60 seconds (1777.60 seconds total)