Starting phenix.real_space_refine on Sat Aug 3 21:04:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y81_39029/08_2024/8y81_39029.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y81_39029/08_2024/8y81_39029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y81_39029/08_2024/8y81_39029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y81_39029/08_2024/8y81_39029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y81_39029/08_2024/8y81_39029.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8y81_39029/08_2024/8y81_39029.cif" } resolution = 2.89 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= 0.058 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 40 5.16 5 C 5713 2.51 5 N 1483 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A TYR 154": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A TYR 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 199": "OE1" <-> "OE2" Residue "A ARG 201": "NH1" <-> "NH2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ASP 89": "OD1" <-> "OD2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "E GLU 158": "OE1" <-> "OE2" Residue "E GLU 159": "OE1" <-> "OE2" Residue "E TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 222": "OE1" <-> "OE2" Residue "E GLU 236": "OE1" <-> "OE2" Residue "E GLU 283": "OE1" <-> "OE2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E GLU 324": "OE1" <-> "OE2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "E PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F GLU 158": "OE1" <-> "OE2" Residue "F TYR 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 179": "OE1" <-> "OE2" Residue "F GLU 283": "OE1" <-> "OE2" Residue "F GLU 324": "OE1" <-> "OE2" Residue "F PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 376": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F GLU 410": "OE1" <-> "OE2" Residue "G ARG 45": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8915 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1729 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 4, 'TRANS': 207} Chain: "B" Number of atoms: 1227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1227 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 1, 'TRANS': 156} Chain: "C" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "E" Number of atoms: 2602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2602 Classifications: {'peptide': 320} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 300} Chain: "F" Number of atoms: 2571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2571 Classifications: {'peptide': 316} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 17, 'TRANS': 295} Chain: "G" Number of atoms: 274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 274 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "T" 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: "A" 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: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'Y01': 1} Classifications: {'undetermined': 1} 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.19, per 1000 atoms: 0.58 Number of scatterers: 8915 At special positions: 0 Unit cell: (148.73, 101.65, 112.35, 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 40 16.00 O 1679 8.00 N 1483 7.00 C 5713 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 49 " - pdb=" SG CYS A 91 " distance=2.05 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 162 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS G 25 " distance=2.03 Simple disulfide: pdb=" SG CYS E 112 " - pdb=" SG CYS F 200 " distance=2.02 Simple disulfide: pdb=" SG CYS E 125 " - pdb=" SG CYS E 184 " distance=2.03 Simple disulfide: pdb=" SG CYS E 230 " - pdb=" SG CYS E 289 " distance=2.03 Simple disulfide: pdb=" SG CYS E 334 " - pdb=" SG CYS E 396 " distance=2.03 Simple disulfide: pdb=" SG CYS F 125 " - pdb=" SG CYS F 184 " distance=2.03 Simple disulfide: pdb=" SG CYS F 230 " - pdb=" SG CYS F 289 " distance=2.02 Simple disulfide: pdb=" SG CYS F 334 " - pdb=" SG CYS F 396 " distance=2.04 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 D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A 301 " - " ASN A 158 " " NAG A 302 " - " ASN A 167 " " NAG D 1 " - " ASN E 265 " " NAG E 502 " - " ASN E 240 " " NAG F 501 " - " ASN F 170 " " NAG H 1 " - " ASN F 265 " " NAG T 1 " - " ASN A 65 " Time building additional restraints: 3.45 Conformation dependent library (CDL) restraints added in 1.5 seconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2070 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 19 sheets defined 29.0% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 213 through 231 removed outlier: 4.272A pdb=" N THR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 228 " --> pdb=" O SER A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 4.027A pdb=" N ILE A 235 " --> pdb=" O SER A 231 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLN A 236 " --> pdb=" O ILE A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 236' Processing helix chain 'B' and resid 51 through 56 removed outlier: 3.642A pdb=" N LYS B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 83 removed outlier: 4.362A pdb=" N GLN B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 88 removed outlier: 3.593A pdb=" N PHE B 88 " --> pdb=" O THR B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 98 Processing helix chain 'B' and resid 99 through 122 removed outlier: 3.662A pdb=" N LEU B 107 " --> pdb=" O TRP B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 160 Processing helix chain 'B' and resid 168 through 205 removed outlier: 3.778A pdb=" N LEU B 187 " --> pdb=" O MET B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 58 Processing helix chain 'E' and resid 173 through 178 Processing helix chain 'E' and resid 216 through 222 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.580A pdb=" N TRP E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 389 Processing helix chain 'F' and resid 173 through 178 Processing helix chain 'F' and resid 204 through 208 Processing helix chain 'F' and resid 216 through 222 Processing helix chain 'F' and resid 277 through 284 Processing helix chain 'F' and resid 385 through 389 Processing helix chain 'G' and resid 25 through 56 removed outlier: 3.693A pdb=" N LEU G 32 " --> pdb=" O LEU G 28 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU G 39 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE G 48 " --> pdb=" O CYS G 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLN G 49 " --> pdb=" O ARG G 45 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 6.538A pdb=" N ILE A 39 " --> pdb=" O MET A 107 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N TRP A 62 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 111 through 115 Processing sheet with id=AA4, first strand: chain 'A' and resid 119 through 121 removed outlier: 5.987A pdb=" N SER A 171 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS A 145 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N HIS A 173 " --> pdb=" O TYR A 143 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N TYR A 143 " --> pdb=" O HIS A 173 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N THR A 175 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL A 141 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 141 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR A 152 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N TYR A 143 " --> pdb=" O PHE A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 119 through 121 Processing sheet with id=AA6, first strand: chain 'E' and resid 104 through 109 removed outlier: 5.273A pdb=" N ALA E 163 " --> pdb=" O GLY E 129 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU E 162 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU E 158 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N SER E 164 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 144 through 145 Processing sheet with id=AA8, first strand: chain 'E' and resid 209 through 213 removed outlier: 5.463A pdb=" N THR E 229 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU E 274 " --> pdb=" O THR E 229 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N LEU E 231 " --> pdb=" O SER E 272 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N SER E 272 " --> pdb=" O LEU E 231 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N LEU E 233 " --> pdb=" O ILE E 270 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N ILE E 270 " --> pdb=" O LEU E 233 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 242 through 246 Processing sheet with id=AB1, first strand: chain 'E' and resid 315 through 319 removed outlier: 3.815A pdb=" N THR E 333 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE E 375 " --> pdb=" O ASN E 338 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 315 through 319 removed outlier: 3.815A pdb=" N THR E 333 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N PHE E 375 " --> pdb=" O ASN E 338 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB4, first strand: chain 'F' and resid 104 through 109 removed outlier: 4.765A pdb=" N ALA F 163 " --> pdb=" O GLY F 129 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N TYR F 166 " --> pdb=" O LEU F 155 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LEU F 155 " --> pdb=" O TYR F 166 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 135 through 141 Processing sheet with id=AB6, first strand: chain 'F' and resid 209 through 213 removed outlier: 3.732A pdb=" N ASP F 234 " --> pdb=" O THR F 268 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR F 268 " --> pdb=" O ASP F 234 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 242 through 246 Processing sheet with id=AB8, first strand: chain 'F' and resid 315 through 319 removed outlier: 3.672A pdb=" N THR F 333 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE F 375 " --> pdb=" O ASN F 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 315 through 319 removed outlier: 3.672A pdb=" N THR F 333 " --> pdb=" O PHE F 319 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N PHE F 375 " --> pdb=" O ASN F 338 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 345 through 348 460 hydrogen bonds defined for protein. 1227 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2042 1.33 - 1.45: 2026 1.45 - 1.57: 5003 1.57 - 1.70: 1 1.70 - 1.82: 49 Bond restraints: 9121 Sorted by residual: bond pdb=" CAX Y01 B 601 " pdb=" OAH Y01 B 601 " ideal model delta sigma weight residual 1.248 1.342 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" N GLU A 199 " pdb=" CA GLU A 199 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.15e-02 7.56e+03 7.63e+00 bond pdb=" CB PRO E 103 " pdb=" CG PRO E 103 " ideal model delta sigma weight residual 1.492 1.611 -0.119 5.00e-02 4.00e+02 5.67e+00 bond pdb=" C1 NAG E 502 " pdb=" O5 NAG E 502 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.69e+00 bond pdb=" C1 NAG A 302 " pdb=" O5 NAG A 302 " ideal model delta sigma weight residual 1.406 1.449 -0.043 2.00e-02 2.50e+03 4.68e+00 ... (remaining 9116 not shown) Histogram of bond angle deviations from ideal: 94.27 - 102.26: 12 102.26 - 110.25: 2205 110.25 - 118.24: 4964 118.24 - 126.23: 5021 126.23 - 134.22: 181 Bond angle restraints: 12383 Sorted by residual: angle pdb=" CA PRO E 103 " pdb=" N PRO E 103 " pdb=" CD PRO E 103 " ideal model delta sigma weight residual 112.00 104.98 7.02 1.40e+00 5.10e-01 2.52e+01 angle pdb=" C TYR F 368 " pdb=" N ASN F 369 " pdb=" CA ASN F 369 " ideal model delta sigma weight residual 121.54 130.69 -9.15 1.91e+00 2.74e-01 2.29e+01 angle pdb=" C GLN E 390 " pdb=" N THR E 391 " pdb=" CA THR E 391 " ideal model delta sigma weight residual 122.46 128.97 -6.51 1.41e+00 5.03e-01 2.13e+01 angle pdb=" C VAL B 127 " pdb=" N ARG B 128 " pdb=" CA ARG B 128 " ideal model delta sigma weight residual 121.54 130.35 -8.81 1.91e+00 2.74e-01 2.13e+01 angle pdb=" C TYR E 368 " pdb=" N ASN E 369 " pdb=" CA ASN E 369 " ideal model delta sigma weight residual 125.02 132.02 -7.00 1.76e+00 3.23e-01 1.58e+01 ... (remaining 12378 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 5267 21.62 - 43.24: 360 43.24 - 64.85: 51 64.85 - 86.47: 28 86.47 - 108.09: 10 Dihedral angle restraints: 5716 sinusoidal: 2532 harmonic: 3184 Sorted by residual: dihedral pdb=" CA ASP A 33 " pdb=" C ASP A 33 " pdb=" N PRO A 34 " pdb=" CA PRO A 34 " ideal model delta harmonic sigma weight residual 180.00 99.19 80.81 0 5.00e+00 4.00e-02 2.61e+02 dihedral pdb=" CA ILE A 198 " pdb=" C ILE A 198 " pdb=" N GLU A 199 " pdb=" CA GLU A 199 " ideal model delta harmonic sigma weight residual 180.00 140.60 39.40 0 5.00e+00 4.00e-02 6.21e+01 dihedral pdb=" CA ASN A 179 " pdb=" C ASN A 179 " pdb=" N LYS A 180 " pdb=" CA LYS A 180 " ideal model delta harmonic sigma weight residual 180.00 143.34 36.66 0 5.00e+00 4.00e-02 5.38e+01 ... (remaining 5713 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 1161 0.074 - 0.148: 254 0.148 - 0.223: 26 0.223 - 0.297: 9 0.297 - 0.371: 2 Chirality restraints: 1452 Sorted by residual: chirality pdb=" CB ILE F 413 " pdb=" CA ILE F 413 " pdb=" CG1 ILE F 413 " pdb=" CG2 ILE F 413 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.44e+00 chirality pdb=" CBH Y01 B 601 " pdb=" CAT Y01 B 601 " pdb=" CAZ Y01 B 601 " pdb=" CBF Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.85 -2.52 -0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CBG Y01 B 601 " pdb=" CAQ Y01 B 601 " pdb=" CBD Y01 B 601 " pdb=" CBI Y01 B 601 " both_signs ideal model delta sigma weight residual False -2.33 -2.62 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 1449 not shown) Planarity restraints: 1526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 198 " -0.027 2.00e-02 2.50e+03 5.31e-02 2.82e+01 pdb=" C ILE A 198 " 0.092 2.00e-02 2.50e+03 pdb=" O ILE A 198 " -0.034 2.00e-02 2.50e+03 pdb=" N GLU A 199 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 154 " 0.022 2.00e-02 2.50e+03 2.50e-02 1.25e+01 pdb=" CG TYR A 154 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR A 154 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 154 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR A 154 " 0.010 2.00e-02 2.50e+03 pdb=" CE2 TYR A 154 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR A 154 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 154 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 33 " 0.047 5.00e-02 4.00e+02 7.29e-02 8.51e+00 pdb=" N PRO A 34 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 34 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 34 " 0.040 5.00e-02 4.00e+02 ... (remaining 1523 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2080 2.80 - 3.32: 7809 3.32 - 3.85: 15182 3.85 - 4.37: 17784 4.37 - 4.90: 30761 Nonbonded interactions: 73616 Sorted by model distance: nonbonded pdb=" O VAL B 78 " pdb=" OG1 THR B 82 " model vdw 2.274 3.040 nonbonded pdb=" O THR B 174 " pdb=" OG1 THR B 178 " model vdw 2.274 3.040 nonbonded pdb=" O ASP E 142 " pdb=" O6 NAG D 1 " model vdw 2.284 3.040 nonbonded pdb=" OD2 ASP E 143 " pdb=" ND1 HIS E 263 " model vdw 2.286 3.120 nonbonded pdb=" OH TYR C 35 " pdb=" OG1 THR G 40 " model vdw 2.287 3.040 ... (remaining 73611 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 24 through 57) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = (chain 'E' and (resid 101 through 416 or resid 502)) selection = chain 'F' } 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: 2.770 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: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 26.680 Find NCS groups from input model: 0.240 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:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 : 0.007 0.119 9121 Z= 0.463 Angle : 0.997 12.122 12383 Z= 0.525 Chirality : 0.063 0.371 1452 Planarity : 0.007 0.073 1519 Dihedral : 16.035 108.091 3613 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.85 % Favored : 96.06 % Rotamer: Outliers : 0.10 % Allowed : 0.61 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.29 % 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: -1.30 (0.24), residues: 1065 helix: -1.51 (0.25), residues: 279 sheet: -0.11 (0.29), residues: 321 loop : -0.83 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 103 HIS 0.011 0.002 HIS F 295 PHE 0.036 0.003 PHE E 117 TYR 0.059 0.003 TYR A 154 ARG 0.004 0.000 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 126 average time/residue: 1.0318 time to fit residues: 140.6390 Evaluate side-chains 83 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.3980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.5980 chunk 95 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN B 134 ASN B 151 ASN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 174 GLN ** F 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 264 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 9121 Z= 0.255 Angle : 0.632 10.306 12383 Z= 0.330 Chirality : 0.046 0.153 1452 Planarity : 0.005 0.062 1519 Dihedral : 11.182 75.612 1504 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.61 % Allowed : 8.27 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.24), residues: 1065 helix: -0.35 (0.27), residues: 282 sheet: -0.00 (0.29), residues: 324 loop : -0.52 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 222 HIS 0.006 0.001 HIS F 295 PHE 0.019 0.002 PHE E 117 TYR 0.017 0.001 TYR G 35 ARG 0.005 0.001 ARG E 330 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 93 time to evaluate : 0.991 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 7 residues processed: 99 average time/residue: 0.9908 time to fit residues: 106.7521 Evaluate side-chains 90 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain E residue 229 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain F residue 343 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 79 optimal weight: 6.9990 chunk 64 optimal weight: 0.0970 chunk 26 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 85 optimal weight: 0.6980 chunk 94 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN F 118 HIS F 264 HIS ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9121 Z= 0.243 Angle : 0.594 10.729 12383 Z= 0.310 Chirality : 0.045 0.149 1452 Planarity : 0.004 0.058 1519 Dihedral : 9.706 74.499 1504 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.92 % Allowed : 10.60 % Favored : 87.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: -0.15 (0.25), residues: 1065 helix: 0.42 (0.29), residues: 273 sheet: 0.01 (0.29), residues: 324 loop : -0.34 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.005 0.001 HIS F 295 PHE 0.016 0.002 PHE E 117 TYR 0.017 0.002 TYR G 35 ARG 0.005 0.000 ARG E 374 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 93 time to evaluate : 0.820 Fit side-chains revert: symmetry clash REVERT: F 279 LYS cc_start: 0.7746 (mtmt) cc_final: 0.7220 (mmtt) REVERT: G 32 LEU cc_start: 0.8137 (mt) cc_final: 0.7765 (mt) outliers start: 19 outliers final: 10 residues processed: 104 average time/residue: 0.9703 time to fit residues: 109.8534 Evaluate side-chains 95 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain F residue 343 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 50 optimal weight: 0.0070 chunk 90 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 350 GLN F 264 HIS ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9121 Z= 0.250 Angle : 0.590 10.625 12383 Z= 0.305 Chirality : 0.045 0.149 1452 Planarity : 0.004 0.056 1519 Dihedral : 8.876 73.694 1504 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.32 % Allowed : 13.42 % Favored : 84.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.05 (0.25), residues: 1065 helix: 0.77 (0.30), residues: 273 sheet: 0.02 (0.28), residues: 324 loop : -0.26 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 PHE 0.023 0.002 PHE A 207 TYR 0.016 0.002 TYR G 35 ARG 0.005 0.000 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 93 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: G 32 LEU cc_start: 0.8168 (mt) cc_final: 0.7713 (mt) outliers start: 23 outliers final: 12 residues processed: 106 average time/residue: 0.9354 time to fit residues: 108.7467 Evaluate side-chains 99 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 0.7980 chunk 57 optimal weight: 0.3980 chunk 1 optimal weight: 0.0980 chunk 75 optimal weight: 0.0020 chunk 41 optimal weight: 0.6980 chunk 86 optimal weight: 0.4980 chunk 70 optimal weight: 0.4980 chunk 0 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 337 GLN E 369 ASN F 109 HIS F 264 HIS ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9121 Z= 0.161 Angle : 0.554 10.048 12383 Z= 0.286 Chirality : 0.044 0.157 1452 Planarity : 0.004 0.056 1519 Dihedral : 8.194 71.835 1504 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 15.84 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.26 (0.25), residues: 1065 helix: 1.04 (0.30), residues: 274 sheet: 0.16 (0.29), residues: 324 loop : -0.22 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 PHE 0.018 0.001 PHE A 207 TYR 0.022 0.001 TYR B 100 ARG 0.005 0.000 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 97 time to evaluate : 0.984 Fit side-chains revert: symmetry clash REVERT: A 175 THR cc_start: 0.8686 (p) cc_final: 0.8416 (t) REVERT: E 315 GLU cc_start: 0.7455 (pm20) cc_final: 0.7174 (pt0) REVERT: F 279 LYS cc_start: 0.7823 (mtmt) cc_final: 0.7304 (mmtt) REVERT: G 32 LEU cc_start: 0.8087 (mt) cc_final: 0.7651 (mt) outliers start: 18 outliers final: 7 residues processed: 106 average time/residue: 0.9040 time to fit residues: 105.1238 Evaluate side-chains 90 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 83 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 337 GLN ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9121 Z= 0.257 Angle : 0.579 10.546 12383 Z= 0.299 Chirality : 0.045 0.151 1452 Planarity : 0.004 0.053 1519 Dihedral : 8.220 72.690 1504 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.32 % Allowed : 16.35 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.25), residues: 1065 helix: 1.08 (0.30), residues: 278 sheet: 0.13 (0.28), residues: 324 loop : -0.16 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.005 0.001 HIS F 295 PHE 0.025 0.002 PHE B 108 TYR 0.016 0.002 TYR G 35 ARG 0.007 0.000 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: E 315 GLU cc_start: 0.7590 (pm20) cc_final: 0.7250 (pt0) outliers start: 23 outliers final: 12 residues processed: 107 average time/residue: 0.9388 time to fit residues: 110.6797 Evaluate side-chains 98 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 61 optimal weight: 0.0570 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 337 GLN F 264 HIS ** F 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9121 Z= 0.242 Angle : 0.569 10.356 12383 Z= 0.295 Chirality : 0.044 0.142 1452 Planarity : 0.004 0.053 1519 Dihedral : 8.105 71.989 1504 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.42 % Allowed : 16.35 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.35 (0.25), residues: 1065 helix: 1.19 (0.30), residues: 278 sheet: 0.13 (0.28), residues: 324 loop : -0.15 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 PHE 0.019 0.002 PHE B 108 TYR 0.015 0.002 TYR B 100 ARG 0.007 0.000 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.017 Fit side-chains revert: symmetry clash REVERT: E 144 ARG cc_start: 0.7368 (ttp-110) cc_final: 0.6752 (ptp-110) REVERT: F 279 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7255 (mmtt) outliers start: 24 outliers final: 12 residues processed: 103 average time/residue: 0.8836 time to fit residues: 99.9868 Evaluate side-chains 99 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 86 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 175 THR Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 0.4980 chunk 79 optimal weight: 6.9990 chunk 92 optimal weight: 0.0060 chunk 96 optimal weight: 1.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 337 GLN F 264 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9121 Z= 0.212 Angle : 0.556 10.191 12383 Z= 0.289 Chirality : 0.044 0.142 1452 Planarity : 0.004 0.053 1519 Dihedral : 7.837 71.583 1504 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.12 % Allowed : 16.75 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.43 (0.26), residues: 1065 helix: 1.29 (0.30), residues: 278 sheet: 0.16 (0.28), residues: 324 loop : -0.11 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 PHE 0.018 0.002 PHE B 108 TYR 0.018 0.001 TYR B 100 ARG 0.006 0.000 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 91 time to evaluate : 0.922 Fit side-chains revert: symmetry clash REVERT: A 175 THR cc_start: 0.8731 (p) cc_final: 0.8459 (t) REVERT: E 144 ARG cc_start: 0.7387 (ttp-110) cc_final: 0.6800 (ptp-110) REVERT: F 279 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7240 (mmtt) outliers start: 21 outliers final: 14 residues processed: 101 average time/residue: 0.8604 time to fit residues: 95.5103 Evaluate side-chains 104 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 89 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain E residue 242 THR Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 96 optimal weight: 0.5980 chunk 56 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 28 optimal weight: 0.0370 chunk 85 optimal weight: 0.0670 chunk 89 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 overall best weight: 0.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 GLN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 337 GLN F 264 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9121 Z= 0.178 Angle : 0.543 9.964 12383 Z= 0.283 Chirality : 0.043 0.140 1452 Planarity : 0.004 0.053 1519 Dihedral : 7.560 71.016 1504 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.92 % Allowed : 16.85 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1065 helix: 1.37 (0.30), residues: 278 sheet: 0.23 (0.28), residues: 324 loop : -0.06 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 PHE 0.018 0.002 PHE A 207 TYR 0.013 0.001 TYR B 100 ARG 0.006 0.000 ARG E 144 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 88 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 175 THR cc_start: 0.8687 (p) cc_final: 0.8421 (t) REVERT: E 144 ARG cc_start: 0.7492 (ttp-110) cc_final: 0.6930 (ptp-110) REVERT: F 279 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7226 (mmtt) outliers start: 19 outliers final: 12 residues processed: 99 average time/residue: 0.8715 time to fit residues: 94.9209 Evaluate side-chains 92 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 104 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 64 optimal weight: 0.0980 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 337 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9121 Z= 0.238 Angle : 0.567 10.229 12383 Z= 0.294 Chirality : 0.044 0.143 1452 Planarity : 0.004 0.052 1519 Dihedral : 7.667 71.589 1504 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.61 % Allowed : 17.05 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.50 (0.26), residues: 1065 helix: 1.38 (0.30), residues: 278 sheet: 0.21 (0.28), residues: 324 loop : -0.10 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.006 0.001 HIS F 295 PHE 0.020 0.002 PHE E 117 TYR 0.023 0.002 TYR B 100 ARG 0.005 0.000 ARG E 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: A 175 THR cc_start: 0.8735 (p) cc_final: 0.8449 (t) REVERT: E 144 ARG cc_start: 0.7434 (ttp-110) cc_final: 0.6846 (ptp-110) REVERT: F 279 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7234 (mmtt) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 0.9261 time to fit residues: 98.4829 Evaluate side-chains 96 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLN Chi-restraints excluded: chain A residue 49 CYS Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain E residue 244 THR Chi-restraints excluded: chain E residue 246 VAL Chi-restraints excluded: chain E residue 298 LYS Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 279 LYS Chi-restraints excluded: chain F residue 343 ASP Chi-restraints excluded: chain F residue 413 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 8.9990 chunk 12 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 83 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 HIS E 153 ASN E 223 ASN E 337 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.174965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.136667 restraints weight = 10171.856| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.17 r_work: 0.3338 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9121 Z= 0.238 Angle : 0.563 10.170 12383 Z= 0.293 Chirality : 0.044 0.144 1452 Planarity : 0.004 0.052 1519 Dihedral : 7.689 71.716 1504 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.72 % Allowed : 17.46 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.30 % Cis-general : 0.10 % Twisted Proline : 2.33 % 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: 0.50 (0.26), residues: 1065 helix: 1.39 (0.31), residues: 275 sheet: 0.19 (0.28), residues: 324 loop : -0.09 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 103 HIS 0.007 0.001 HIS F 295 PHE 0.020 0.002 PHE E 117 TYR 0.019 0.002 TYR B 100 ARG 0.005 0.000 ARG E 144 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2997.14 seconds wall clock time: 53 minutes 34.96 seconds (3214.96 seconds total)