Starting phenix.real_space_refine on Thu Dec 7 22:29:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/12_2023/7uwj_26833.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/12_2023/7uwj_26833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/12_2023/7uwj_26833.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/12_2023/7uwj_26833.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/12_2023/7uwj_26833.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uwj_26833/12_2023/7uwj_26833.pdb" } resolution = 3.2 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= 0.001 sd= 0.024 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 50 5.16 5 C 3338 2.51 5 N 928 2.21 5 O 998 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 5314 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 771 Classifications: {'peptide': 94} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 86} Chain breaks: 1 Chain: "C" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1844 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 771 Classifications: {'peptide': 94} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 86} Chain breaks: 1 Chain: "D" Number of atoms: 1844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1844 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 221} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} 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 Time building chain proxies: 3.55, per 1000 atoms: 0.67 Number of scatterers: 5314 At special positions: 0 Unit cell: (93.731, 95.4352, 107.365, 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 50 16.00 O 998 8.00 N 928 7.00 C 3338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS A 112 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 115 " - pdb=" SG CYS A 170 " distance=2.03 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 102 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 99 " distance=2.03 Simple disulfide: pdb=" SG CYS C 162 " - pdb=" SG CYS C 173 " distance=2.03 Simple disulfide: pdb=" SG CYS C 187 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 257 " - pdb=" SG CYS C 261 " distance=2.03 Simple disulfide: pdb=" SG CYS B 74 " - pdb=" SG CYS B 112 " distance=2.03 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 168 " distance=2.03 Simple disulfide: pdb=" SG CYS B 115 " - pdb=" SG CYS B 170 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 102 " distance=2.03 Simple disulfide: pdb=" SG CYS D 87 " - pdb=" SG CYS D 99 " distance=2.03 Simple disulfide: pdb=" SG CYS D 162 " - pdb=" SG CYS D 173 " distance=2.03 Simple disulfide: pdb=" SG CYS D 187 " - pdb=" SG CYS D 271 " distance=2.03 Simple disulfide: pdb=" SG CYS D 257 " - pdb=" SG CYS D 261 " distance=2.03 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 NAG-ASN " NAG C 301 " - " ASN C 103 " " NAG C 302 " - " ASN C 156 " " NAG C 303 " - " ASN C 197 " " NAG D 301 " - " ASN D 103 " " NAG D 302 " - " ASN D 156 " " NAG D 303 " - " ASN D 197 " Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 970.9 milliseconds 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1252 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 15 sheets defined 3.9% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'C' and resid 31 through 36 removed outlier: 4.060A pdb=" N MET C 35 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU C 36 " --> pdb=" O PRO C 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 31 through 36' Processing helix chain 'C' and resid 170 through 177 removed outlier: 3.616A pdb=" N LYS C 175 " --> pdb=" O LYS C 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 36 removed outlier: 3.913A pdb=" N MET D 35 " --> pdb=" O SER D 31 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N LEU D 36 " --> pdb=" O PRO D 32 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 31 through 36' Processing helix chain 'D' and resid 170 through 175 removed outlier: 4.322A pdb=" N LYS D 175 " --> pdb=" O LYS D 171 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 96 removed outlier: 3.533A pdb=" N HIS A 107 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 95 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU A 105 " --> pdb=" O ASP A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 101 removed outlier: 4.278A pdb=" N ALA A 167 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N HIS A 135 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER A 165 " --> pdb=" O HIS A 135 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN A 137 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N ARG A 163 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 139 " --> pdb=" O LEU A 161 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU A 161 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N TYR A 141 " --> pdb=" O ARG A 159 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N ARG A 159 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.266A pdb=" N MET A 176 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N THR D 267 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS D 264 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 250 " --> pdb=" O HIS D 264 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR D 247 " --> pdb=" O GLN D 212 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE D 211 " --> pdb=" O ILE D 217 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE D 217 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 175 through 176 removed outlier: 7.266A pdb=" N MET A 176 " --> pdb=" O LYS D 265 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N THR D 267 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N HIS D 264 " --> pdb=" O LEU D 250 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU D 250 " --> pdb=" O HIS D 264 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR D 247 " --> pdb=" O GLN D 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 22 through 24 removed outlier: 4.467A pdb=" N GLN C 23 " --> pdb=" O ASN C 103 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA C 83 " --> pdb=" O ILE C 141 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE C 141 " --> pdb=" O ALA C 83 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE C 157 " --> pdb=" O TYR C 134 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 136 " --> pdb=" O VAL C 155 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 49 through 55 removed outlier: 3.877A pdb=" N VAL C 53 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU C 65 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N THR C 55 " --> pdb=" O SER C 63 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N SER C 63 " --> pdb=" O THR C 55 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N ILE C 64 " --> pdb=" O PRO C 127 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N MET C 66 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 185 through 187 Processing sheet with id=AA8, first strand: chain 'C' and resid 206 through 207 removed outlier: 3.596A pdb=" N VAL C 222 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 216 through 219 removed outlier: 3.563A pdb=" N ILE C 217 " --> pdb=" O ILE C 211 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ILE C 211 " --> pdb=" O ILE C 217 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR C 247 " --> pdb=" O GLN C 212 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ARG C 263 " --> pdb=" O MET B 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 90 through 96 Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 101 removed outlier: 3.600A pdb=" N LEU B 101 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N PHE B 140 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N ASN B 129 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N CYS B 170 " --> pdb=" O ASN B 129 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N GLU B 131 " --> pdb=" O CYS B 168 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N CYS B 168 " --> pdb=" O GLU B 131 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEU B 133 " --> pdb=" O LEU B 166 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N HIS B 135 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N VAL B 139 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 47 through 55 removed outlier: 3.522A pdb=" N SER D 69 " --> pdb=" O ARG D 49 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER D 63 " --> pdb=" O THR D 55 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ILE D 64 " --> pdb=" O PRO D 127 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N MET D 66 " --> pdb=" O GLY D 125 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N GLY D 125 " --> pdb=" O MET D 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE D 121 " --> pdb=" O TRP D 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 96 through 100 removed outlier: 3.667A pdb=" N GLY D 90 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA D 83 " --> pdb=" O ILE D 141 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N HIS D 139 " --> pdb=" O LYS D 85 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE D 136 " --> pdb=" O VAL D 155 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL D 155 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ALA D 138 " --> pdb=" O MET D 153 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N MET D 153 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 132 through 133 removed outlier: 4.088A pdb=" N THR D 132 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 185 through 187 removed outlier: 3.966A pdb=" N PHE D 198 " --> pdb=" O ALA D 233 " (cutoff:3.500A) 116 hydrogen bonds defined for protein. 312 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: 1.26 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1719 1.34 - 1.46: 1238 1.46 - 1.58: 2411 1.58 - 1.70: 0 1.70 - 1.82: 66 Bond restraints: 5434 Sorted by residual: bond pdb=" C VAL C 22 " pdb=" N GLN C 23 " ideal model delta sigma weight residual 1.331 1.378 -0.047 1.34e-02 5.57e+03 1.24e+01 bond pdb=" N VAL C 100 " pdb=" CA VAL C 100 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.24e+00 bond pdb=" N ARG C 101 " pdb=" CA ARG C 101 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.21e-02 6.83e+03 7.33e+00 bond pdb=" N GLY C 25 " pdb=" CA GLY C 25 " ideal model delta sigma weight residual 1.449 1.483 -0.034 1.45e-02 4.76e+03 5.51e+00 bond pdb=" C1 NAG D 303 " pdb=" O5 NAG D 303 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 5429 not shown) Histogram of bond angle deviations from ideal: 98.64 - 105.71: 178 105.71 - 112.78: 2942 112.78 - 119.85: 1667 119.85 - 126.92: 2518 126.92 - 133.99: 73 Bond angle restraints: 7378 Sorted by residual: angle pdb=" CA VAL C 22 " pdb=" C VAL C 22 " pdb=" N GLN C 23 " ideal model delta sigma weight residual 116.34 108.39 7.95 1.28e+00 6.10e-01 3.86e+01 angle pdb=" O VAL C 22 " pdb=" C VAL C 22 " pdb=" N GLN C 23 " ideal model delta sigma weight residual 123.10 129.18 -6.08 1.17e+00 7.31e-01 2.70e+01 angle pdb=" CA ASN C 103 " pdb=" CB ASN C 103 " pdb=" CG ASN C 103 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" C TYR C 104 " pdb=" CA TYR C 104 " pdb=" CB TYR C 104 " ideal model delta sigma weight residual 109.38 117.94 -8.56 1.80e+00 3.09e-01 2.26e+01 angle pdb=" CA ASN C 103 " pdb=" C ASN C 103 " pdb=" O ASN C 103 " ideal model delta sigma weight residual 121.89 116.84 5.05 1.17e+00 7.31e-01 1.86e+01 ... (remaining 7373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 3088 17.85 - 35.70: 255 35.70 - 53.55: 49 53.55 - 71.40: 14 71.40 - 89.26: 2 Dihedral angle restraints: 3408 sinusoidal: 1476 harmonic: 1932 Sorted by residual: dihedral pdb=" CB CYS C 162 " pdb=" SG CYS C 162 " pdb=" SG CYS C 173 " pdb=" CB CYS C 173 " ideal model delta sinusoidal sigma weight residual 93.00 -177.74 -89.26 1 1.00e+01 1.00e-02 9.48e+01 dihedral pdb=" CB CYS D 162 " pdb=" SG CYS D 162 " pdb=" SG CYS D 173 " pdb=" CB CYS D 173 " ideal model delta sinusoidal sigma weight residual 93.00 162.08 -69.08 1 1.00e+01 1.00e-02 6.17e+01 dihedral pdb=" CB CYS A 115 " pdb=" SG CYS A 115 " pdb=" SG CYS A 170 " pdb=" CB CYS A 170 " ideal model delta sinusoidal sigma weight residual 93.00 149.03 -56.03 1 1.00e+01 1.00e-02 4.24e+01 ... (remaining 3405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 830 0.112 - 0.224: 14 0.224 - 0.337: 0 0.337 - 0.449: 0 0.449 - 0.561: 2 Chirality restraints: 846 Sorted by residual: chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 103 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CA GLN C 23 " pdb=" N GLN C 23 " pdb=" C GLN C 23 " pdb=" CB GLN C 23 " both_signs ideal model delta sigma weight residual False 2.51 2.98 -0.47 2.00e-01 2.50e+01 5.48e+00 chirality pdb=" CA VAL C 100 " pdb=" N VAL C 100 " pdb=" C VAL C 100 " pdb=" CB VAL C 100 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 ... (remaining 843 not shown) Planarity restraints: 946 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 41 " 0.072 5.00e-02 4.00e+02 1.09e-01 1.89e+01 pdb=" N PRO C 42 " -0.188 5.00e-02 4.00e+02 pdb=" CA PRO C 42 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO C 42 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 80 " 0.066 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO B 81 " -0.177 5.00e-02 4.00e+02 pdb=" CA PRO B 81 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO B 81 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 181 " 0.065 5.00e-02 4.00e+02 9.57e-02 1.46e+01 pdb=" N PRO D 182 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO D 182 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO D 182 " 0.052 5.00e-02 4.00e+02 ... (remaining 943 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 321 2.73 - 3.27: 4823 3.27 - 3.82: 7946 3.82 - 4.36: 9021 4.36 - 4.90: 15828 Nonbonded interactions: 37939 Sorted by model distance: nonbonded pdb=" O ALA D 138 " pdb=" OG SER D 152 " model vdw 2.189 2.440 nonbonded pdb=" N SER A 77 " pdb=" O SER A 84 " model vdw 2.203 2.520 nonbonded pdb=" OE1 GLN A 119 " pdb=" NH1 ARG B 127 " model vdw 2.284 2.520 nonbonded pdb=" OE1 GLN C 249 " pdb=" NH1 ARG C 263 " model vdw 2.287 2.520 nonbonded pdb=" OD1 ASP D 47 " pdb=" NH1 ARG D 49 " model vdw 2.290 2.520 ... (remaining 37934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.660 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 18.640 Find NCS groups from input model: 0.270 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5904 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 : 0.004 0.079 5434 Z= 0.249 Angle : 0.795 9.705 7378 Z= 0.462 Chirality : 0.051 0.561 846 Planarity : 0.009 0.109 940 Dihedral : 13.198 70.187 2108 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 13.04 % 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: -2.14 (0.31), residues: 640 helix: -3.23 (0.93), residues: 12 sheet: -1.09 (0.31), residues: 266 loop : -1.60 (0.29), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 70 HIS 0.004 0.001 HIS D 213 PHE 0.010 0.001 PHE C 108 TYR 0.017 0.001 TYR A 162 ARG 0.007 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2237 time to fit residues: 31.2916 Evaluate side-chains 106 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 chunk 32 optimal weight: 0.0030 chunk 25 optimal weight: 0.0770 chunk 50 optimal weight: 0.0170 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 37 optimal weight: 0.3980 chunk 58 optimal weight: 0.9980 overall best weight: 0.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 ASN C 147 ASN B 129 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5844 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5434 Z= 0.146 Angle : 0.581 9.403 7378 Z= 0.291 Chirality : 0.043 0.164 846 Planarity : 0.006 0.075 940 Dihedral : 6.028 43.690 848 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.17 % Allowed : 7.02 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.94 (0.31), residues: 640 helix: -2.50 (1.04), residues: 16 sheet: -0.96 (0.31), residues: 268 loop : -1.46 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 70 HIS 0.003 0.001 HIS C 139 PHE 0.010 0.001 PHE C 157 TYR 0.014 0.001 TYR C 253 ARG 0.006 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 96 average time/residue: 0.2173 time to fit residues: 26.1261 Evaluate side-chains 98 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 92 time to evaluate : 0.614 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0541 time to fit residues: 1.4322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.0050 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 67 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5434 Z= 0.205 Angle : 0.617 10.297 7378 Z= 0.312 Chirality : 0.044 0.155 846 Planarity : 0.006 0.063 940 Dihedral : 5.971 40.950 848 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.00 % Allowed : 8.86 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.99 (0.31), residues: 640 helix: -2.41 (1.08), residues: 16 sheet: -0.95 (0.31), residues: 266 loop : -1.54 (0.29), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 70 HIS 0.004 0.001 HIS B 107 PHE 0.015 0.001 PHE D 198 TYR 0.013 0.001 TYR C 253 ARG 0.003 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 97 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 99 average time/residue: 0.2207 time to fit residues: 27.0200 Evaluate side-chains 98 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 93 time to evaluate : 0.615 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0558 time to fit residues: 1.3602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 30 optimal weight: 0.0980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.2980 chunk 55 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- 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: 0.5924 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5434 Z= 0.161 Angle : 0.563 9.977 7378 Z= 0.284 Chirality : 0.042 0.160 846 Planarity : 0.005 0.049 940 Dihedral : 5.563 41.844 848 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.67 % Allowed : 10.03 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.95 (0.31), residues: 640 helix: -2.48 (1.07), residues: 16 sheet: -0.92 (0.32), residues: 252 loop : -1.50 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 70 HIS 0.002 0.001 HIS B 107 PHE 0.012 0.001 PHE D 198 TYR 0.013 0.001 TYR C 253 ARG 0.005 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 95 average time/residue: 0.2592 time to fit residues: 31.1413 Evaluate side-chains 99 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.552 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1292 time to fit residues: 1.8655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 0.2980 chunk 42 optimal weight: 0.0050 chunk 31 optimal weight: 1.9990 chunk 55 optimal weight: 0.0020 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 overall best weight: 0.6004 ------------------------------------------------------------------------------- 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: 0.5958 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5434 Z= 0.187 Angle : 0.594 10.127 7378 Z= 0.297 Chirality : 0.043 0.157 846 Planarity : 0.005 0.048 940 Dihedral : 5.680 41.127 848 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.00 % Allowed : 10.87 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.98 (0.31), residues: 640 helix: -2.51 (1.08), residues: 16 sheet: -1.00 (0.32), residues: 252 loop : -1.47 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 70 HIS 0.004 0.001 HIS B 107 PHE 0.013 0.001 PHE D 198 TYR 0.013 0.001 TYR C 253 ARG 0.006 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 94 average time/residue: 0.2169 time to fit residues: 25.6598 Evaluate side-chains 92 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.609 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0610 time to fit residues: 1.1702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.0060 chunk 15 optimal weight: 0.9980 chunk 61 optimal weight: 0.0040 chunk 51 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 20 optimal weight: 0.0050 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.3222 ------------------------------------------------------------------------------- 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: 0.5914 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 5434 Z= 0.154 Angle : 0.554 9.712 7378 Z= 0.277 Chirality : 0.042 0.159 846 Planarity : 0.005 0.045 940 Dihedral : 5.342 41.895 848 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 1.67 % Allowed : 12.04 % Favored : 86.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.85 (0.31), residues: 640 helix: -2.52 (1.07), residues: 16 sheet: -0.92 (0.32), residues: 252 loop : -1.38 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 70 HIS 0.002 0.000 HIS B 107 PHE 0.010 0.001 PHE D 198 TYR 0.010 0.001 TYR C 253 ARG 0.006 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 94 average time/residue: 0.2074 time to fit residues: 24.5308 Evaluate side-chains 97 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 0.628 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1264 time to fit residues: 1.9147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 34 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 18 optimal weight: 0.0870 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6009 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5434 Z= 0.241 Angle : 0.640 10.743 7378 Z= 0.320 Chirality : 0.044 0.178 846 Planarity : 0.005 0.049 940 Dihedral : 6.144 44.681 848 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 1.51 % Allowed : 12.04 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -2.00 (0.31), residues: 640 helix: -2.33 (1.08), residues: 16 sheet: -1.05 (0.32), residues: 252 loop : -1.47 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP D 70 HIS 0.006 0.001 HIS B 107 PHE 0.014 0.001 PHE D 198 TYR 0.012 0.001 TYR B 106 ARG 0.007 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 96 average time/residue: 0.2298 time to fit residues: 27.3552 Evaluate side-chains 95 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.650 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0576 time to fit residues: 1.4620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.2980 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5434 Z= 0.251 Angle : 0.653 11.001 7378 Z= 0.329 Chirality : 0.045 0.191 846 Planarity : 0.005 0.057 940 Dihedral : 6.293 43.358 848 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 1.51 % Allowed : 13.04 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -2.11 (0.31), residues: 640 helix: -2.21 (1.08), residues: 16 sheet: -1.09 (0.32), residues: 252 loop : -1.58 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP D 70 HIS 0.007 0.001 HIS B 114 PHE 0.015 0.001 PHE D 198 TYR 0.013 0.002 TYR B 106 ARG 0.006 0.001 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 94 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 96 average time/residue: 0.2314 time to fit residues: 27.5931 Evaluate side-chains 97 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 90 time to evaluate : 0.656 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0645 time to fit residues: 1.6687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 0.2980 chunk 34 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 60 optimal weight: 0.0270 chunk 28 optimal weight: 0.0050 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5963 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5434 Z= 0.164 Angle : 0.579 9.966 7378 Z= 0.289 Chirality : 0.043 0.157 846 Planarity : 0.005 0.048 940 Dihedral : 5.627 42.548 848 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.84 % Allowed : 13.55 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -1.99 (0.31), residues: 640 helix: -2.25 (1.05), residues: 16 sheet: -0.99 (0.32), residues: 252 loop : -1.51 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 70 HIS 0.003 0.001 HIS B 107 PHE 0.010 0.001 PHE D 198 TYR 0.008 0.001 TYR B 141 ARG 0.008 0.000 ARG D 232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 90 average time/residue: 0.2382 time to fit residues: 26.3802 Evaluate side-chains 90 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 87 time to evaluate : 0.618 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0610 time to fit residues: 1.1995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.0040 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5434 Z= 0.208 Angle : 0.611 10.500 7378 Z= 0.306 Chirality : 0.043 0.179 846 Planarity : 0.005 0.051 940 Dihedral : 5.976 44.648 848 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 0.67 % Allowed : 14.38 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -2.04 (0.31), residues: 640 helix: -2.11 (1.09), residues: 16 sheet: -1.02 (0.32), residues: 252 loop : -1.55 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 70 HIS 0.005 0.001 HIS B 107 PHE 0.012 0.001 PHE D 198 TYR 0.010 0.001 TYR B 141 ARG 0.005 0.000 ARG D 232 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1280 Ramachandran restraints generated. 640 Oldfield, 0 Emsley, 640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 91 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 92 average time/residue: 0.2403 time to fit residues: 27.3603 Evaluate side-chains 93 residues out of total 600 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 90 time to evaluate : 0.672 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0517 time to fit residues: 1.0914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 44 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.215772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.189499 restraints weight = 7819.062| |-----------------------------------------------------------------------------| r_work (start): 0.4430 rms_B_bonded: 3.16 r_work: 0.4309 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6314 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5434 Z= 0.188 Angle : 0.598 10.201 7378 Z= 0.298 Chirality : 0.043 0.155 846 Planarity : 0.005 0.049 940 Dihedral : 5.740 43.116 848 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 0.50 % Allowed : 14.21 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.04 % 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: -2.02 (0.31), residues: 640 helix: -2.08 (1.09), residues: 16 sheet: -1.00 (0.32), residues: 252 loop : -1.55 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 70 HIS 0.004 0.001 HIS B 107 PHE 0.010 0.001 PHE D 198 TYR 0.009 0.001 TYR B 141 ARG 0.005 0.000 ARG D 232 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1693.92 seconds wall clock time: 31 minutes 5.08 seconds (1865.08 seconds total)