Starting phenix.real_space_refine on Mon Mar 11 05:07:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/03_2024/8d85_27247.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/03_2024/8d85_27247.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/03_2024/8d85_27247.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/03_2024/8d85_27247.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/03_2024/8d85_27247.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d85_27247/03_2024/8d85_27247.pdb" } resolution = 3.81 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= 0.000 sd= 0.019 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 31 5.16 5 C 4527 2.51 5 N 1197 2.21 5 O 1338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 73": "NH1" <-> "NH2" Residue "C TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C PHE 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C GLU 213": "OE1" <-> "OE2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 85": "OE1" <-> "OE2" Residue "D ASP 89": "OD1" <-> "OD2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 175": "OE1" <-> "OE2" Residue "D TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 220": "OE1" <-> "OE2" Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 59": "OD1" <-> "OD2" Residue "A GLU 65": "OE1" <-> "OE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A GLU 192": "OE1" <-> "OE2" Residue "A GLU 197": "OE1" <-> "OE2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "B TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 151": "OE1" <-> "OE2" Residue "B ARG 176": "NH1" <-> "NH2" Residue "B ASP 177": "OD1" <-> "OD2" Residue "B TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 201": "OE1" <-> "OE2" Residue "B ASP 210": "OD1" <-> "OD2" Residue "B PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 315": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7093 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 1590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1590 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 178} Chain: "D" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1452 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 9, 'TRANS': 167} Chain breaks: 1 Chain: "A" Number of atoms: 1524 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1524 Classifications: {'peptide': 191} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 172} Chain: "B" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2373 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 16, 'TRANS': 279} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 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 Chain: "A" 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 Chain: "B" 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: 4.18, per 1000 atoms: 0.59 Number of scatterers: 7093 At special positions: 0 Unit cell: (107.5, 104.06, 139.32, 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 31 16.00 O 1338 8.00 N 1197 7.00 C 4527 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 46 " distance=2.03 Simple disulfide: pdb=" SG CYS C 79 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 52 " distance=2.03 Simple disulfide: pdb=" SG CYS A 164 " - pdb=" SG CYS A 208 " distance=2.03 Simple disulfide: pdb=" SG CYS B 28 " - pdb=" SG CYS B 54 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 144 " distance=2.03 Simple disulfide: pdb=" SG CYS B 172 " - pdb=" SG CYS B 182 " 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 BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " NAG-ASN " NAG A 601 " - " ASN A 76 " " NAG B 701 " - " ASN B 227 " " NAG B 702 " - " ASN B 157 " " NAG B 703 " - " ASN B 131 " " NAG C 301 " - " ASN C 105 " " NAG E 1 " - " ASN A 51 " " NAG F 1 " - " ASN B 83 " " NAG G 1 " - " ASN B 43 " Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.4 seconds 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1646 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 18 sheets defined 17.8% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'D' and resid 42 through 73 Processing helix chain 'D' and resid 93 through 100 Processing helix chain 'D' and resid 103 through 124 Proline residue: D 115 - end of helix Processing helix chain 'D' and resid 130 through 158 Processing helix chain 'D' and resid 166 through 179 Processing helix chain 'D' and resid 196 through 225 Processing helix chain 'B' and resid 51 through 58 Processing helix chain 'B' and resid 247 through 251 removed outlier: 4.305A pdb=" N SER B 251 " --> pdb=" O SER B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.643A pdb=" N ALA B 278 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 43 through 46 removed outlier: 4.160A pdb=" N CYS C 46 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS C 89 " --> pdb=" O CYS C 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.649A pdb=" N ILE C 63 " --> pdb=" O THR C 107 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 103 " --> pdb=" O ARG C 67 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE C 121 " --> pdb=" O TYR C 102 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 136 through 138 removed outlier: 3.686A pdb=" N LEU C 145 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 178 through 183 removed outlier: 6.205A pdb=" N TYR C 165 " --> pdb=" O PRO C 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.674A pdb=" N GLU A 65 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR A 108 " --> pdb=" O GLU A 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 102 through 105 removed outlier: 3.526A pdb=" N VAL A 105 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 118 " --> pdb=" O VAL A 105 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 132 through 139 removed outlier: 3.829A pdb=" N ARG A 132 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N HIS A 150 " --> pdb=" O GLY A 134 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASP A 136 " --> pdb=" O THR A 148 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N THR A 148 " --> pdb=" O ASP A 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 177 through 178 removed outlier: 3.869A pdb=" N LEU A 183 " --> pdb=" O CYS A 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 177 through 178 Processing sheet with id=AB1, first strand: chain 'A' and resid 202 through 204 removed outlier: 3.561A pdb=" N LEU A 224 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 37 through 38 removed outlier: 3.957A pdb=" N VAL B 38 " --> pdb=" O ILE B 121 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 45 through 47 Processing sheet with id=AB4, first strand: chain 'B' and resid 73 through 74 removed outlier: 4.735A pdb=" N TRP B 67 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL B 66 " --> pdb=" O ASN B 104 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN B 104 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLN B 113 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 181 through 183 removed outlier: 4.364A pdb=" N CYS B 182 " --> pdb=" O CYS B 144 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N CYS B 144 " --> pdb=" O CYS B 182 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG B 143 " --> pdb=" O ILE B 135 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ASP B 147 " --> pdb=" O ASN B 131 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ASN B 131 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N LYS B 221 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL B 136 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.864A pdb=" N LYS B 161 " --> pdb=" O TRP B 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP B 197 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 195 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 172 through 173 removed outlier: 3.864A pdb=" N LYS B 161 " --> pdb=" O TRP B 197 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TRP B 197 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 195 " --> pdb=" O GLU B 163 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ILE B 194 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE B 214 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N VAL B 196 " --> pdb=" O ILE B 212 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B 212 " --> pdb=" O VAL B 196 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 229 through 231 removed outlier: 3.622A pdb=" N THR B 243 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS B 241 " --> pdb=" O ILE B 231 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 270 through 271 removed outlier: 3.987A pdb=" N TYR B 295 " --> pdb=" O GLY B 319 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLY B 319 " --> pdb=" O TYR B 295 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA B 317 " --> pdb=" O PHE B 297 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 549 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: 1.78 Time building geometry restraints manager: 2.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2263 1.34 - 1.46: 1724 1.46 - 1.58: 3259 1.58 - 1.70: 0 1.70 - 1.82: 43 Bond restraints: 7289 Sorted by residual: bond pdb=" C ASP D 102 " pdb=" N PRO D 103 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.08e-02 8.57e+03 3.24e+00 bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.21e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.20e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.05e+00 bond pdb=" C1 NAG B 702 " pdb=" O5 NAG B 702 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.83e+00 ... (remaining 7284 not shown) Histogram of bond angle deviations from ideal: 100.86 - 107.48: 410 107.48 - 114.11: 4159 114.11 - 120.73: 2687 120.73 - 127.36: 2568 127.36 - 133.98: 117 Bond angle restraints: 9941 Sorted by residual: angle pdb=" CA LEU A 68 " pdb=" CB LEU A 68 " pdb=" CG LEU A 68 " ideal model delta sigma weight residual 116.30 126.43 -10.13 3.50e+00 8.16e-02 8.37e+00 angle pdb=" N SER B 32 " pdb=" CA SER B 32 " pdb=" C SER B 32 " ideal model delta sigma weight residual 109.81 115.62 -5.81 2.21e+00 2.05e-01 6.92e+00 angle pdb=" C VAL C 109 " pdb=" N HIS C 110 " pdb=" CA HIS C 110 " ideal model delta sigma weight residual 121.80 116.20 5.60 2.44e+00 1.68e-01 5.28e+00 angle pdb=" C LEU A 198 " pdb=" N ALA A 199 " pdb=" CA ALA A 199 " ideal model delta sigma weight residual 122.08 125.21 -3.13 1.47e+00 4.63e-01 4.53e+00 angle pdb=" C ILE B 31 " pdb=" N SER B 32 " pdb=" CA SER B 32 " ideal model delta sigma weight residual 121.80 116.99 4.81 2.44e+00 1.68e-01 3.89e+00 ... (remaining 9936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.69: 4205 21.69 - 43.38: 204 43.38 - 65.07: 46 65.07 - 86.76: 21 86.76 - 108.45: 52 Dihedral angle restraints: 4528 sinusoidal: 1995 harmonic: 2533 Sorted by residual: dihedral pdb=" CB CYS C 35 " pdb=" SG CYS C 35 " pdb=" SG CYS C 46 " pdb=" CB CYS C 46 " ideal model delta sinusoidal sigma weight residual -86.00 -43.34 -42.66 1 1.00e+01 1.00e-02 2.54e+01 dihedral pdb=" CA SER B 32 " pdb=" C SER B 32 " pdb=" N PRO B 33 " pdb=" CA PRO B 33 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" C1 NAG G 1 " pdb=" C2 NAG G 1 " pdb=" C3 NAG G 1 " pdb=" O3 NAG G 1 " ideal model delta sinusoidal sigma weight residual -175.09 -66.64 -108.45 1 3.00e+01 1.11e-03 1.40e+01 ... (remaining 4525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 891 0.041 - 0.082: 136 0.082 - 0.122: 92 0.122 - 0.163: 7 0.163 - 0.204: 2 Chirality restraints: 1128 Sorted by residual: chirality pdb=" C1 NAG E 1 " pdb=" ND2 ASN A 51 " pdb=" C2 NAG E 1 " pdb=" O5 NAG E 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1 NAG C 301 " pdb=" ND2 ASN C 105 " pdb=" C2 NAG C 301 " pdb=" O5 NAG C 301 " both_signs ideal model delta sigma weight residual False -2.40 -2.23 -0.17 2.00e-01 2.50e+01 7.51e-01 chirality pdb=" C1 NAG B 701 " pdb=" ND2 ASN B 227 " pdb=" C2 NAG B 701 " pdb=" O5 NAG B 701 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-01 2.50e+01 6.44e-01 ... (remaining 1125 not shown) Planarity restraints: 1264 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 102 " -0.026 5.00e-02 4.00e+02 3.92e-02 2.46e+00 pdb=" N PRO D 103 " 0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 40 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO C 41 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 41 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 41 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 272 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO B 273 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO B 273 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 273 " -0.018 5.00e-02 4.00e+02 ... (remaining 1261 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 2379 2.87 - 3.37: 6114 3.37 - 3.88: 10679 3.88 - 4.39: 10827 4.39 - 4.90: 19504 Nonbonded interactions: 49503 Sorted by model distance: nonbonded pdb=" NE2 GLN C 81 " pdb=" O SER C 86 " model vdw 2.357 2.520 nonbonded pdb=" NH2 ARG C 168 " pdb=" OE1 GLN C 202 " model vdw 2.367 2.520 nonbonded pdb=" NE1 TRP C 166 " pdb=" OE1 GLN C 206 " model vdw 2.372 2.520 nonbonded pdb=" OE1 GLU B 34 " pdb=" OG SER B 35 " model vdw 2.374 2.440 nonbonded pdb=" ND2 ASN B 246 " pdb=" OG SER B 282 " model vdw 2.381 2.520 ... (remaining 49498 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 'E' selection = chain 'F' selection = chain 'G' } 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=0.00 max=1.00 mean=0.99 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: 3.150 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: 11.620 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 22.400 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6271 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 : 0.003 0.041 7289 Z= 0.167 Angle : 0.531 10.127 9941 Z= 0.261 Chirality : 0.040 0.204 1128 Planarity : 0.003 0.039 1256 Dihedral : 19.549 108.448 2858 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.09 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -2.45 (0.25), residues: 855 helix: 0.17 (0.39), residues: 154 sheet: -0.72 (0.39), residues: 174 loop : -2.67 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP A 115 HIS 0.001 0.000 HIS D 117 PHE 0.005 0.000 PHE D 116 TYR 0.005 0.000 TYR B 79 ARG 0.001 0.000 ARG D 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 193 time to evaluate : 0.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 LEU cc_start: 0.8169 (pt) cc_final: 0.7776 (mt) REVERT: C 110 HIS cc_start: 0.2159 (m170) cc_final: 0.1914 (m90) REVERT: D 144 LEU cc_start: 0.8883 (tp) cc_final: 0.8462 (tt) REVERT: B 146 TRP cc_start: 0.8176 (p90) cc_final: 0.7824 (p90) outliers start: 0 outliers final: 0 residues processed: 193 average time/residue: 0.2475 time to fit residues: 59.3268 Evaluate side-chains 109 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 109 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 HIS ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN D 154 GLN ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 96 GLN A 159 HIS A 167 HIS ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN B 211 HIS B 258 ASN B 260 GLN B 271 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 7289 Z= 0.216 Angle : 0.698 9.568 9941 Z= 0.315 Chirality : 0.050 0.517 1128 Planarity : 0.005 0.082 1256 Dihedral : 17.767 88.071 1167 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 1.30 % Allowed : 14.92 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % 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: -1.57 (0.27), residues: 855 helix: 1.88 (0.42), residues: 148 sheet: -0.89 (0.35), residues: 195 loop : -2.11 (0.24), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 217 HIS 0.004 0.001 HIS B 211 PHE 0.017 0.001 PHE C 188 TYR 0.013 0.001 TYR B 79 ARG 0.004 0.001 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 110 HIS cc_start: 0.2484 (m170) cc_final: 0.2109 (m90) REVERT: C 198 ARG cc_start: 0.6597 (mtm-85) cc_final: 0.6310 (mtm-85) REVERT: D 144 LEU cc_start: 0.8830 (tp) cc_final: 0.8526 (tt) REVERT: B 146 TRP cc_start: 0.8454 (p90) cc_final: 0.8241 (p90) REVERT: B 239 ILE cc_start: 0.7117 (mm) cc_final: 0.6858 (pt) REVERT: B 302 MET cc_start: 0.6098 (OUTLIER) cc_final: 0.5883 (ptt) outliers start: 10 outliers final: 6 residues processed: 128 average time/residue: 0.2052 time to fit residues: 34.5525 Evaluate side-chains 107 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 133 GLU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain A residue 99 MET Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 302 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 76 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 150 HIS ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 GLN ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7019 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 7289 Z= 0.322 Angle : 0.776 8.619 9941 Z= 0.370 Chirality : 0.051 0.487 1128 Planarity : 0.006 0.106 1256 Dihedral : 13.476 77.587 1167 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.67 % Favored : 93.22 % Rotamer: Outliers : 3.37 % Allowed : 19.07 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.34 (0.27), residues: 855 helix: 2.21 (0.42), residues: 148 sheet: -0.81 (0.31), residues: 233 loop : -2.04 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 310 HIS 0.007 0.002 HIS A 67 PHE 0.020 0.002 PHE C 188 TYR 0.023 0.002 TYR A 205 ARG 0.010 0.001 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.8008 (tp40) cc_final: 0.7688 (tp40) REVERT: D 77 ASN cc_start: 0.6582 (t0) cc_final: 0.6256 (t0) REVERT: B 146 TRP cc_start: 0.8746 (p90) cc_final: 0.8330 (p90) REVERT: B 302 MET cc_start: 0.6543 (ptt) cc_final: 0.6260 (ptt) outliers start: 26 outliers final: 17 residues processed: 141 average time/residue: 0.2030 time to fit residues: 37.6014 Evaluate side-chains 111 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 94 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 301 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 76 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 51 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 82 optimal weight: 0.3980 chunk 73 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 154 GLN ** A 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7289 Z= 0.192 Angle : 0.655 8.922 9941 Z= 0.299 Chirality : 0.046 0.393 1128 Planarity : 0.005 0.086 1256 Dihedral : 11.408 67.211 1167 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.96 % Favored : 93.92 % Rotamer: Outliers : 2.72 % Allowed : 19.71 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -1.08 (0.28), residues: 855 helix: 2.55 (0.43), residues: 148 sheet: -0.86 (0.31), residues: 241 loop : -1.80 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 217 HIS 0.003 0.001 HIS D 117 PHE 0.018 0.001 PHE B 72 TYR 0.015 0.001 TYR B 261 ARG 0.003 0.000 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.7863 (tp40) cc_final: 0.7612 (tp40) REVERT: D 140 MET cc_start: 0.8270 (tmm) cc_final: 0.8027 (tmm) REVERT: B 76 LYS cc_start: 0.7653 (OUTLIER) cc_final: 0.7254 (tttp) REVERT: B 146 TRP cc_start: 0.8649 (p90) cc_final: 0.8227 (p90) outliers start: 21 outliers final: 12 residues processed: 109 average time/residue: 0.1870 time to fit residues: 27.7116 Evaluate side-chains 105 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 265 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 46 optimal weight: 9.9990 chunk 1 optimal weight: 0.0370 chunk 61 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 chunk 56 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 73 optimal weight: 8.9990 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 71 GLN B 59 HIS ** B 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7289 Z= 0.174 Angle : 0.635 14.687 9941 Z= 0.286 Chirality : 0.045 0.382 1128 Planarity : 0.005 0.093 1256 Dihedral : 9.914 56.420 1167 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.08 % Favored : 93.80 % Rotamer: Outliers : 2.72 % Allowed : 21.01 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.84 (0.28), residues: 855 helix: 2.72 (0.42), residues: 148 sheet: -0.64 (0.32), residues: 227 loop : -1.65 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 89 HIS 0.003 0.001 HIS B 59 PHE 0.019 0.001 PHE B 72 TYR 0.013 0.001 TYR B 79 ARG 0.004 0.000 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.7862 (tp40) cc_final: 0.7634 (tp40) REVERT: D 140 MET cc_start: 0.8227 (tmm) cc_final: 0.7987 (tmm) REVERT: B 76 LYS cc_start: 0.7566 (OUTLIER) cc_final: 0.7186 (tttp) outliers start: 21 outliers final: 14 residues processed: 107 average time/residue: 0.2015 time to fit residues: 28.9014 Evaluate side-chains 101 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 265 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 73 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 48 optimal weight: 0.0980 chunk 20 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 38 optimal weight: 0.0270 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7289 Z= 0.171 Angle : 0.643 11.461 9941 Z= 0.289 Chirality : 0.046 0.446 1128 Planarity : 0.005 0.079 1256 Dihedral : 8.550 57.964 1167 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.73 % Favored : 94.15 % Rotamer: Outliers : 2.59 % Allowed : 22.05 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.74 (0.28), residues: 855 helix: 2.79 (0.42), residues: 148 sheet: -0.52 (0.32), residues: 229 loop : -1.61 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 89 HIS 0.003 0.001 HIS D 117 PHE 0.020 0.001 PHE B 72 TYR 0.012 0.001 TYR B 79 ARG 0.004 0.000 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 93 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 64 GLN cc_start: 0.7872 (tp40) cc_final: 0.7610 (tp40) REVERT: D 140 MET cc_start: 0.8237 (tmm) cc_final: 0.7992 (tmm) REVERT: A 217 TRP cc_start: 0.7739 (m100) cc_final: 0.6746 (m100) REVERT: B 76 LYS cc_start: 0.7607 (OUTLIER) cc_final: 0.7246 (tttp) REVERT: B 146 TRP cc_start: 0.8588 (p90) cc_final: 0.8198 (p90) REVERT: B 260 GLN cc_start: 0.7219 (mt0) cc_final: 0.7003 (mt0) outliers start: 20 outliers final: 14 residues processed: 106 average time/residue: 0.1910 time to fit residues: 27.5823 Evaluate side-chains 101 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain B residue 265 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 9 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 49 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 GLN B 258 ASN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.5400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7289 Z= 0.286 Angle : 0.744 11.056 9941 Z= 0.350 Chirality : 0.049 0.435 1128 Planarity : 0.005 0.099 1256 Dihedral : 7.892 58.901 1167 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.07 % Favored : 91.81 % Rotamer: Outliers : 4.02 % Allowed : 22.05 % Favored : 73.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.81 % Cis-general : 0.00 % Twisted Proline : 1.56 % 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: -0.98 (0.28), residues: 855 helix: 2.56 (0.42), residues: 148 sheet: -0.70 (0.33), residues: 222 loop : -1.74 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 156 HIS 0.004 0.001 HIS B 211 PHE 0.019 0.002 PHE B 72 TYR 0.019 0.002 TYR B 79 ARG 0.007 0.001 ARG D 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1710 Ramachandran restraints generated. 855 Oldfield, 0 Emsley, 855 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: D 64 GLN cc_start: 0.7974 (tp40) cc_final: 0.7742 (tp40) REVERT: D 77 ASN cc_start: 0.6942 (t0) cc_final: 0.6731 (t0) REVERT: D 95 GLN cc_start: 0.8430 (mm110) cc_final: 0.8075 (mm-40) REVERT: D 132 MET cc_start: 0.7149 (ppp) cc_final: 0.6896 (ppp) REVERT: D 140 MET cc_start: 0.8302 (tmm) cc_final: 0.8024 (tmm) REVERT: A 182 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.6183 (mm-30) REVERT: A 210 MET cc_start: 0.6042 (mmp) cc_final: 0.5709 (mmm) REVERT: A 217 TRP cc_start: 0.8087 (m100) cc_final: 0.6851 (m100) REVERT: B 76 LYS cc_start: 0.7657 (OUTLIER) cc_final: 0.7372 (tttp) REVERT: B 146 TRP cc_start: 0.8685 (p90) cc_final: 0.8208 (p90) outliers start: 31 outliers final: 21 residues processed: 118 average time/residue: 0.1639 time to fit residues: 27.0854 Evaluate side-chains 115 residues out of total 771 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 92 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 45 ASP Chi-restraints excluded: chain C residue 75 HIS Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain C residue 193 VAL Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 125 THR Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 195 VAL Chi-restraints excluded: chain A residue 143 ASP Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain B residue 76 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 119 THR Chi-restraints excluded: chain B residue 164 TRP Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 265 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.8566 > 50: distance: 43 - 139: 28.662 distance: 58 - 118: 22.064 distance: 96 - 97: 7.540 distance: 96 - 235: 4.796 distance: 97 - 98: 6.947 distance: 97 - 100: 14.783 distance: 98 - 99: 14.280 distance: 98 - 101: 9.441 distance: 99 - 232: 20.223 distance: 101 - 102: 4.433 distance: 102 - 103: 7.837 distance: 102 - 105: 6.929 distance: 103 - 104: 9.720 distance: 103 - 108: 15.204 distance: 105 - 106: 8.747 distance: 105 - 107: 7.805 distance: 108 - 109: 6.396 distance: 109 - 110: 7.118 distance: 109 - 112: 15.322 distance: 110 - 111: 21.134 distance: 110 - 115: 30.837 distance: 112 - 113: 20.172 distance: 112 - 114: 9.313 distance: 115 - 116: 18.648 distance: 116 - 117: 23.268 distance: 116 - 119: 15.270 distance: 117 - 118: 7.238 distance: 117 - 125: 19.729 distance: 120 - 121: 7.928 distance: 120 - 122: 13.994 distance: 121 - 123: 7.742 distance: 122 - 124: 7.871 distance: 123 - 124: 8.532 distance: 125 - 126: 15.210 distance: 126 - 127: 22.434 distance: 126 - 129: 13.391 distance: 127 - 128: 31.098 distance: 127 - 139: 13.210 distance: 129 - 130: 11.263 distance: 130 - 131: 5.608 distance: 130 - 132: 5.081 distance: 131 - 133: 7.733 distance: 132 - 134: 6.245 distance: 132 - 135: 4.617 distance: 133 - 134: 6.630 distance: 134 - 136: 6.705 distance: 135 - 137: 5.735 distance: 136 - 138: 6.414 distance: 137 - 138: 8.248 distance: 139 - 140: 5.731 distance: 140 - 141: 28.565 distance: 140 - 143: 20.315 distance: 141 - 142: 7.568 distance: 141 - 144: 10.671 distance: 144 - 145: 18.728 distance: 144 - 150: 18.399 distance: 145 - 146: 6.541 distance: 145 - 148: 13.096 distance: 146 - 147: 4.860 distance: 146 - 151: 3.381 distance: 148 - 149: 10.845 distance: 149 - 150: 5.332 distance: 151 - 152: 12.279 distance: 151 - 157: 14.808 distance: 152 - 153: 14.090 distance: 152 - 155: 6.779 distance: 153 - 154: 20.620 distance: 153 - 158: 27.111 distance: 155 - 156: 21.653 distance: 156 - 157: 15.420 distance: 158 - 159: 20.686 distance: 159 - 160: 18.733 distance: 159 - 162: 27.869 distance: 160 - 161: 25.036 distance: 160 - 165: 13.132 distance: 162 - 163: 12.220 distance: 162 - 164: 10.171 distance: 165 - 166: 18.808 distance: 166 - 167: 16.636 distance: 166 - 169: 22.384 distance: 167 - 179: 20.475 distance: 169 - 170: 12.258 distance: 170 - 171: 3.134 distance: 170 - 172: 5.098 distance: 171 - 173: 8.429 distance: 172 - 174: 7.384 distance: 172 - 175: 7.807 distance: 174 - 176: 6.135 distance: 175 - 177: 7.250 distance: 176 - 178: 10.064 distance: 177 - 178: 7.600