Starting phenix.real_space_refine on Thu Mar 14 15:52:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/03_2024/7sq0_25373_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/03_2024/7sq0_25373.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/03_2024/7sq0_25373.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/03_2024/7sq0_25373.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/03_2024/7sq0_25373_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7sq0_25373/03_2024/7sq0_25373_updated.pdb" } resolution = 3.7 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 54 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4 5.49 5 Mg 2 5.21 5 S 32 5.16 5 C 3089 2.51 5 N 814 2.21 5 O 932 1.98 5 H 4286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 176": "OE1" <-> "OE2" Residue "A TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 229": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 258": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 293": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 295": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 324": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 330": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 341": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 89": "OE1" <-> "OE2" Residue "B ASP 134": "OD1" <-> "OD2" Residue "B PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 176": "OE1" <-> "OE2" Residue "B GLU 186": "OE1" <-> "OE2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "B ARG 229": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 258": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 291": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 293": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 295": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 319": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 324": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 330": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 341": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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: 9160 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 4480 Classifications: {'peptide': 306} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 291} Chain breaks: 3 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'UNK:plan-1': 19, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "B" Number of atoms: 4485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 4485 Classifications: {'peptide': 302} Modifications used: {'NH3': 1} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain breaks: 3 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'UNK:plan-1': 18} Unresolved non-hydrogen planarities: 18 Chain: "C" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 138 Classifications: {'peptide': 22} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 21} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 1, ' ZN': 1, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3490 SG CYS A 287 30.096 41.595 78.100 1.00 78.54 S ATOM 3529 SG CYS A 290 30.245 44.327 76.040 1.00 79.84 S ATOM 7977 SG CYS B 287 27.060 45.006 78.102 1.00 78.23 S ATOM 8016 SG CYS B 290 26.901 42.269 76.059 1.00 79.43 S Time building chain proxies: 4.79, per 1000 atoms: 0.52 Number of scatterers: 9160 At special positions: 0 Unit cell: (58.022, 87.466, 91.796, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 4 15.00 Mg 2 11.99 O 932 8.00 N 814 7.00 C 3089 6.00 H 4286 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.63 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 500 " pdb="ZN ZN A 500 " - pdb=" SG CYS B 290 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 290 " pdb="ZN ZN A 500 " - pdb=" SG CYS A 287 " pdb="ZN ZN A 500 " - pdb=" SG CYS B 287 " Number of angles added : 6 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1210 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 3 sheets defined 54.6% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 6 through 10 removed outlier: 3.662A pdb=" N ASP A 10 " --> pdb=" O HIS A 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 6 through 10' Processing helix chain 'A' and resid 27 through 41 Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.507A pdb=" N MET A 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 116 removed outlier: 3.614A pdb=" N UNK A 105 " --> pdb=" O UNK A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 140 through 154 Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.564A pdb=" N LEU A 172 " --> pdb=" O THR A 168 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 3.515A pdb=" N GLU A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 233 removed outlier: 3.516A pdb=" N ASP A 225 " --> pdb=" O TYR A 221 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 226 " --> pdb=" O PRO A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 266 removed outlier: 3.790A pdb=" N LEU A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 307 removed outlier: 3.719A pdb=" N LYS A 299 " --> pdb=" O ARG A 295 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N TYR A 300 " --> pdb=" O MET A 296 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ASP A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 332 removed outlier: 3.871A pdb=" N ASP A 331 " --> pdb=" O ALA A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 337 No H-bonds generated for 'chain 'A' and resid 334 through 337' Processing helix chain 'B' and resid 6 through 10 removed outlier: 3.654A pdb=" N ASP B 10 " --> pdb=" O HIS B 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 6 through 10' Processing helix chain 'B' and resid 27 through 41 Processing helix chain 'B' and resid 58 through 62 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 98 through 113 removed outlier: 3.659A pdb=" N UNK B 102 " --> pdb=" O UNK B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 134 removed outlier: 3.723A pdb=" N PHE B 131 " --> pdb=" O CYS B 127 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 133 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASP B 134 " --> pdb=" O SER B 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 127 through 134' Processing helix chain 'B' and resid 140 through 154 Processing helix chain 'B' and resid 168 through 188 removed outlier: 3.537A pdb=" N LEU B 172 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ARG B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Proline residue: B 178 - end of helix removed outlier: 3.581A pdb=" N LYS B 183 " --> pdb=" O GLU B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 251 through 266 removed outlier: 3.787A pdb=" N LEU B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 307 removed outlier: 3.724A pdb=" N LYS B 299 " --> pdb=" O ARG B 295 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N TYR B 300 " --> pdb=" O MET B 296 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASP B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 332 removed outlier: 3.869A pdb=" N ASP B 331 " --> pdb=" O ALA B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 337 No H-bonds generated for 'chain 'B' and resid 334 through 337' Processing helix chain 'C' and resid 263 through 282 removed outlier: 3.562A pdb=" N TYR C 280 " --> pdb=" O ILE C 276 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TYR C 281 " --> pdb=" O ILE C 277 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL C 282 " --> pdb=" O GLY C 278 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 312 through 315 removed outlier: 4.918A pdb=" N ALA A 272 " --> pdb=" O PHE A 242 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLY A 244 " --> pdb=" O ALA A 272 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N VAL A 243 " --> pdb=" O TRP A 16 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N PHE A 18 " --> pdb=" O VAL A 243 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N VAL A 245 " --> pdb=" O PHE A 18 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY A 20 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 9.322A pdb=" N ILE A 247 " --> pdb=" O GLY A 20 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL A 161 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N PHE A 19 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N PHE A 163 " --> pdb=" O PHE A 19 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N GLY A 21 " --> pdb=" O PHE A 163 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 48 " --> pdb=" O ILE A 162 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N ASP A 164 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N LEU A 50 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 16 through 21 removed outlier: 7.650A pdb=" N ALA B 272 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 9.157A pdb=" N CYS B 246 " --> pdb=" O ALA B 272 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 274 " --> pdb=" O CYS B 246 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ASN B 312 " --> pdb=" O ILE B 273 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N ILE B 275 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 314 " --> pdb=" O ILE B 275 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 48 through 51 195 hydrogen bonds defined for protein. 573 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 6.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4274 1.03 - 1.23: 12 1.23 - 1.42: 2072 1.42 - 1.61: 2850 1.61 - 1.81: 50 Bond restraints: 9258 Sorted by residual: bond pdb=" C4 ADP B 401 " pdb=" C5 ADP B 401 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4 ADP A 401 " pdb=" C5 ADP A 401 " ideal model delta sigma weight residual 1.490 1.382 0.108 2.00e-02 2.50e+03 2.93e+01 bond pdb=" C5 ADP B 401 " pdb=" C6 ADP B 401 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.71e+01 bond pdb=" C5 ADP A 401 " pdb=" C6 ADP A 401 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C8 ADP B 401 " pdb=" N7 ADP B 401 " ideal model delta sigma weight residual 1.350 1.309 0.041 2.00e-02 2.50e+03 4.17e+00 ... (remaining 9253 not shown) Histogram of bond angle deviations from ideal: 69.60 - 82.47: 13 82.47 - 95.35: 0 95.35 - 108.22: 2156 108.22 - 121.10: 12414 121.10 - 133.98: 1926 Bond angle restraints: 16509 Sorted by residual: angle pdb=" C PRO A 222 " pdb=" CA PRO A 222 " pdb=" HA PRO A 222 " ideal model delta sigma weight residual 109.00 69.60 39.40 3.00e+00 1.11e-01 1.73e+02 angle pdb=" CB LEU C 272 " pdb=" CA LEU C 272 " pdb=" HA LEU C 272 " ideal model delta sigma weight residual 109.00 73.92 35.08 3.00e+00 1.11e-01 1.37e+02 angle pdb=" CB LYS A 223 " pdb=" CA LYS A 223 " pdb=" HA LYS A 223 " ideal model delta sigma weight residual 109.00 74.23 34.77 3.00e+00 1.11e-01 1.34e+02 angle pdb=" C LYS A 223 " pdb=" CA LYS A 223 " pdb=" HA LYS A 223 " ideal model delta sigma weight residual 109.00 74.47 34.53 3.00e+00 1.11e-01 1.32e+02 angle pdb=" C LEU C 272 " pdb=" CA LEU C 272 " pdb=" HA LEU C 272 " ideal model delta sigma weight residual 109.00 74.77 34.23 3.00e+00 1.11e-01 1.30e+02 ... (remaining 16504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.01: 4343 28.01 - 56.02: 77 56.02 - 84.03: 20 84.03 - 112.03: 0 112.03 - 140.04: 6 Dihedral angle restraints: 4446 sinusoidal: 2288 harmonic: 2158 Sorted by residual: dihedral pdb=" C5' ADP A 401 " pdb=" O5' ADP A 401 " pdb=" PA ADP A 401 " pdb=" O2A ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 159.96 140.04 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C5' ADP B 401 " pdb=" O5' ADP B 401 " pdb=" PA ADP B 401 " pdb=" O2A ADP B 401 " ideal model delta sinusoidal sigma weight residual 300.00 160.15 139.85 1 2.00e+01 2.50e-03 4.23e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual 300.00 179.63 120.37 1 2.00e+01 2.50e-03 3.61e+01 ... (remaining 4443 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 732 0.084 - 0.168: 45 0.168 - 0.252: 0 0.252 - 0.336: 2 0.336 - 0.420: 3 Chirality restraints: 782 Sorted by residual: chirality pdb=" CA PRO A 222 " pdb=" N PRO A 222 " pdb=" C PRO A 222 " pdb=" CB PRO A 222 " both_signs ideal model delta sigma weight residual False 2.72 2.30 0.42 2.00e-01 2.50e+01 4.41e+00 chirality pdb=" CA LEU C 272 " pdb=" N LEU C 272 " pdb=" C LEU C 272 " pdb=" CB LEU C 272 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CA LYS A 223 " pdb=" N LYS A 223 " pdb=" C LYS A 223 " pdb=" CB LYS A 223 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.24e+00 ... (remaining 779 not shown) Planarity restraints: 1384 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 285 " 0.010 5.00e-02 4.00e+02 1.46e-02 3.40e-01 pdb=" N PRO A 286 " -0.025 5.00e-02 4.00e+02 pdb=" CA PRO A 286 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO A 286 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 285 " 0.009 5.00e-02 4.00e+02 1.44e-02 3.30e-01 pdb=" N PRO B 286 " -0.025 5.00e-02 4.00e+02 pdb=" CA PRO B 286 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO B 286 " 0.008 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 247 " 0.009 5.00e-02 4.00e+02 1.39e-02 3.07e-01 pdb=" N PRO A 248 " -0.024 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " 0.007 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " 0.008 5.00e-02 4.00e+02 ... (remaining 1381 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 645 2.22 - 2.82: 18741 2.82 - 3.41: 21257 3.41 - 4.01: 27893 4.01 - 4.60: 43961 Nonbonded interactions: 112497 Sorted by model distance: nonbonded pdb=" H LYS A 223 " pdb=" HA LYS A 223 " model vdw 1.630 1.816 nonbonded pdb=" O GLY B 26 " pdb=" HG1 THR B 30 " model vdw 1.698 1.850 nonbonded pdb=" O PRO A 43 " pdb="HD21 ASN A 78 " model vdw 1.709 1.850 nonbonded pdb=" O GLN C 262 " pdb=" H LEU C 266 " model vdw 1.710 1.850 nonbonded pdb=" O PRO B 43 " pdb="HD22 ASN B 78 " model vdw 1.712 1.850 ... (remaining 112492 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 116 or resid 126 through 131 or (resid 132 and ( \ name N or name CA or name C or name O or name CB )) or resid 133 through 189 or \ resid 221 through 346 or resid 501)) selection = (chain 'B' and (resid 1 through 88 or (resid 89 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 90 through 136 or (resid \ 137 and (name N or name CA or name C or name O or name CB or name CG or name CD1 \ or name CD2 or name CE1 or name CE2 or name CZ )) or resid 138 through 184 or ( \ resid 185 and (name N or name CA or name C or name O or name CB or name CG or na \ me CD1 or name CD2 or name H or name HA )) or resid 186 through 222 or (resid 22 \ 3 and (name N or name CA or name C or name O or name CB or name CG or name CD or \ name CE or name NZ or name H or name HA )) or resid 224 through 345 or (resid 3 \ 46 and (name N or name CA or name C or name O or name CB )) or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.150 Extract box with map and model: 6.410 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 34.480 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 4972 Z= 0.239 Angle : 0.678 13.259 6761 Z= 0.284 Chirality : 0.045 0.420 782 Planarity : 0.001 0.015 858 Dihedral : 13.617 140.043 1765 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.91 (0.32), residues: 579 helix: -1.97 (0.26), residues: 275 sheet: -2.09 (0.47), residues: 86 loop : -1.48 (0.44), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 344 HIS 0.001 0.000 HIS A 56 PHE 0.004 0.001 PHE B 62 TYR 0.005 0.001 TYR A 340 ARG 0.001 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 0.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 LYS cc_start: 0.8633 (mmmt) cc_final: 0.8352 (ttmm) REVERT: A 165 THR cc_start: 0.9253 (p) cc_final: 0.8964 (t) REVERT: A 235 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7540 (mtt90) REVERT: B 151 LYS cc_start: 0.8630 (mmmt) cc_final: 0.8343 (ttmm) REVERT: B 165 THR cc_start: 0.9217 (p) cc_final: 0.8918 (t) REVERT: B 183 LYS cc_start: 0.8292 (tppt) cc_final: 0.8045 (ttpt) REVERT: B 235 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7631 (mtp-110) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.3777 time to fit residues: 48.2821 Evaluate side-chains 76 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 29 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN B 156 ASN B 261 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4972 Z= 0.182 Angle : 0.559 6.410 6761 Z= 0.266 Chirality : 0.046 0.396 782 Planarity : 0.003 0.018 858 Dihedral : 12.128 144.201 687 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.39 % Allowed : 5.92 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.35), residues: 579 helix: -0.21 (0.30), residues: 282 sheet: -1.52 (0.50), residues: 86 loop : -0.61 (0.48), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 16 HIS 0.002 0.001 HIS A 6 PHE 0.006 0.001 PHE B 174 TYR 0.005 0.001 TYR B 340 ARG 0.002 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 LYS cc_start: 0.8463 (tppt) cc_final: 0.8252 (ttpt) outliers start: 2 outliers final: 1 residues processed: 81 average time/residue: 0.2888 time to fit residues: 31.3010 Evaluate side-chains 66 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4972 Z= 0.153 Angle : 0.531 6.440 6761 Z= 0.248 Chirality : 0.045 0.396 782 Planarity : 0.003 0.023 858 Dihedral : 11.314 136.199 687 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.39 % Allowed : 9.07 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.36), residues: 579 helix: 0.66 (0.31), residues: 283 sheet: -1.15 (0.51), residues: 86 loop : -0.46 (0.47), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 144 HIS 0.001 0.000 HIS B 6 PHE 0.016 0.001 PHE A 311 TYR 0.008 0.001 TYR B 254 ARG 0.001 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 69 average time/residue: 0.2983 time to fit residues: 27.5544 Evaluate side-chains 63 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4972 Z= 0.179 Angle : 0.536 6.275 6761 Z= 0.248 Chirality : 0.046 0.394 782 Planarity : 0.003 0.027 858 Dihedral : 11.478 174.707 687 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.99 % Allowed : 9.07 % Favored : 89.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.37), residues: 579 helix: 1.27 (0.32), residues: 281 sheet: -0.82 (0.54), residues: 90 loop : -0.29 (0.48), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 144 HIS 0.002 0.001 HIS B 56 PHE 0.006 0.001 PHE A 277 TYR 0.011 0.001 TYR A 254 ARG 0.001 0.000 ARG B 295 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7543 (p0) cc_final: 0.7054 (p0) REVERT: A 312 ASN cc_start: 0.8227 (OUTLIER) cc_final: 0.7609 (t0) outliers start: 5 outliers final: 2 residues processed: 73 average time/residue: 0.2616 time to fit residues: 25.5295 Evaluate side-chains 69 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 66 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 312 ASN Chi-restraints excluded: chain B residue 84 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.0670 chunk 51 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 chunk 11 optimal weight: 20.0000 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4972 Z= 0.161 Angle : 0.519 6.079 6761 Z= 0.240 Chirality : 0.046 0.397 782 Planarity : 0.003 0.027 858 Dihedral : 10.261 167.452 687 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.59 % Allowed : 10.26 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.37), residues: 579 helix: 1.49 (0.32), residues: 283 sheet: -0.57 (0.55), residues: 90 loop : -0.25 (0.47), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP A 144 HIS 0.001 0.000 HIS A 6 PHE 0.006 0.001 PHE B 242 TYR 0.009 0.001 TYR B 254 ARG 0.000 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7603 (p0) cc_final: 0.7142 (p0) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 0.2902 time to fit residues: 26.6341 Evaluate side-chains 68 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 236 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4972 Z= 0.138 Angle : 0.512 6.317 6761 Z= 0.233 Chirality : 0.045 0.397 782 Planarity : 0.003 0.026 858 Dihedral : 8.493 127.451 687 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.20 % Allowed : 11.05 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.37), residues: 579 helix: 1.69 (0.32), residues: 284 sheet: -0.42 (0.56), residues: 90 loop : -0.19 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 144 HIS 0.001 0.000 HIS B 56 PHE 0.004 0.001 PHE B 146 TYR 0.009 0.001 TYR B 254 ARG 0.000 0.000 ARG B 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7585 (p0) cc_final: 0.7125 (p0) REVERT: A 338 LYS cc_start: 0.8235 (pttt) cc_final: 0.7970 (mmmm) outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.3277 time to fit residues: 28.4090 Evaluate side-chains 66 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 11 optimal weight: 9.9990 overall best weight: 0.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4972 Z= 0.134 Angle : 0.508 5.770 6761 Z= 0.231 Chirality : 0.045 0.396 782 Planarity : 0.003 0.025 858 Dihedral : 7.916 116.052 687 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.39 % Allowed : 10.85 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.17 (0.37), residues: 579 helix: 1.84 (0.32), residues: 283 sheet: -0.22 (0.56), residues: 90 loop : -0.15 (0.46), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP A 144 HIS 0.001 0.000 HIS B 271 PHE 0.005 0.001 PHE B 146 TYR 0.009 0.001 TYR A 254 ARG 0.001 0.000 ARG A 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 67 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 141 ASP cc_start: 0.7604 (p0) cc_final: 0.7162 (p0) REVERT: A 338 LYS cc_start: 0.8223 (pttt) cc_final: 0.7980 (mmmm) outliers start: 2 outliers final: 2 residues processed: 65 average time/residue: 0.3317 time to fit residues: 28.3883 Evaluate side-chains 65 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 MET Chi-restraints excluded: chain B residue 236 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 10.0000 chunk 29 optimal weight: 1.9990 chunk 5 optimal weight: 0.0270 chunk 46 optimal weight: 0.0670 chunk 54 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 4972 Z= 0.158 Angle : 0.521 6.878 6761 Z= 0.238 Chirality : 0.046 0.397 782 Planarity : 0.003 0.025 858 Dihedral : 7.855 112.522 687 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.39 % Allowed : 11.05 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.27 (0.37), residues: 579 helix: 1.92 (0.31), residues: 282 sheet: -0.14 (0.57), residues: 90 loop : -0.11 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 144 HIS 0.001 0.001 HIS B 6 PHE 0.007 0.001 PHE B 146 TYR 0.007 0.001 TYR B 254 ARG 0.001 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 144 TRP cc_start: 0.7686 (m100) cc_final: 0.7387 (m100) REVERT: A 338 LYS cc_start: 0.8229 (pttt) cc_final: 0.7991 (mmmm) outliers start: 2 outliers final: 1 residues processed: 63 average time/residue: 0.3322 time to fit residues: 27.3942 Evaluate side-chains 63 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 55 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 40 optimal weight: 10.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4972 Z= 0.180 Angle : 0.527 5.637 6761 Z= 0.245 Chirality : 0.046 0.399 782 Planarity : 0.003 0.025 858 Dihedral : 7.964 112.572 687 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.20 % Allowed : 11.24 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.26 (0.37), residues: 579 helix: 1.92 (0.31), residues: 282 sheet: -0.07 (0.58), residues: 90 loop : -0.17 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 144 HIS 0.002 0.001 HIS B 6 PHE 0.006 0.001 PHE B 146 TYR 0.007 0.001 TYR B 254 ARG 0.001 0.000 ARG B 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.8244 (pttt) cc_final: 0.8005 (mmmm) outliers start: 1 outliers final: 1 residues processed: 62 average time/residue: 0.3188 time to fit residues: 25.7813 Evaluate side-chains 59 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 39 optimal weight: 0.0170 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.7022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4972 Z= 0.132 Angle : 0.509 5.650 6761 Z= 0.231 Chirality : 0.045 0.398 782 Planarity : 0.002 0.022 858 Dihedral : 7.596 107.247 687 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.20 % Allowed : 10.45 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.58 (0.37), residues: 579 helix: 2.22 (0.32), residues: 282 sheet: 0.00 (0.58), residues: 90 loop : -0.05 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 144 HIS 0.001 0.000 HIS B 6 PHE 0.006 0.001 PHE B 146 TYR 0.007 0.001 TYR B 254 ARG 0.001 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1158 Ramachandran restraints generated. 579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 185 is missing expected H atoms. Skipping. Residue LYS 223 is missing expected H atoms. Skipping. Residue VAL 184 is missing expected H atoms. Skipping. Residue LEU 266 is missing expected H atoms. Skipping. Residue VAL 267 is missing expected H atoms. Skipping. Residue ILE 270 is missing expected H atoms. Skipping. Residue ALA 271 is missing expected H atoms. Skipping. Residue LEU 272 is missing expected H atoms. Skipping. Residue ILE 273 is missing expected H atoms. Skipping. Residue LEU 274 is missing expected H atoms. Skipping. Residue LEU 275 is missing expected H atoms. Skipping. Residue ILE 276 is missing expected H atoms. Skipping. Residue ILE 277 is missing expected H atoms. Skipping. Residue ILE 279 is missing expected H atoms. Skipping. Residue TYR 280 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 63 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 338 LYS cc_start: 0.8200 (pttt) cc_final: 0.7976 (mmmm) outliers start: 1 outliers final: 1 residues processed: 63 average time/residue: 0.3391 time to fit residues: 27.7344 Evaluate side-chains 63 residues out of total 529 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 140 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.088100 restraints weight = 23782.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.092167 restraints weight = 12438.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.094817 restraints weight = 8304.002| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4972 Z= 0.182 Angle : 0.530 5.694 6761 Z= 0.248 Chirality : 0.046 0.400 782 Planarity : 0.003 0.023 858 Dihedral : 7.808 109.989 687 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.20 % Allowed : 10.65 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.53 (0.37), residues: 579 helix: 2.17 (0.31), residues: 282 sheet: 0.02 (0.58), residues: 90 loop : -0.06 (0.46), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 144 HIS 0.002 0.001 HIS B 6 PHE 0.006 0.001 PHE A 277 TYR 0.007 0.001 TYR B 254 ARG 0.001 0.000 ARG B 293 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2435.36 seconds wall clock time: 43 minutes 23.90 seconds (2603.90 seconds total)