Starting phenix.real_space_refine on Fri Jan 19 04:20:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcq_22817/01_2024/7kcq_22817.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcq_22817/01_2024/7kcq_22817.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcq_22817/01_2024/7kcq_22817.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcq_22817/01_2024/7kcq_22817.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcq_22817/01_2024/7kcq_22817.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcq_22817/01_2024/7kcq_22817.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 5 Type Number sf(0) Gaussians Zn 8 6.06 5 S 56 5.16 5 C 6548 2.51 5 N 1752 2.21 5 O 1968 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A GLU 77": "OE1" <-> "OE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 19": "OE1" <-> "OE2" Residue "B GLU 77": "OE1" <-> "OE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 127": "OE1" <-> "OE2" Residue "B GLU 147": "OE1" <-> "OE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B GLU 208": "OE1" <-> "OE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 236": "OD1" <-> "OD2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C GLU 77": "OE1" <-> "OE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 127": "OE1" <-> "OE2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "C GLU 208": "OE1" <-> "OE2" Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ASP 236": "OD1" <-> "OD2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 77": "OE1" <-> "OE2" Residue "D TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 127": "OE1" <-> "OE2" Residue "D GLU 147": "OE1" <-> "OE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D GLU 208": "OE1" <-> "OE2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ASP 236": "OD1" <-> "OD2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 10332 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 333} Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 333} Chain: "C" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 333} Chain: "D" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2581 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 333} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 340 SG CYS A 43 37.825 61.223 54.909 1.00 31.48 S ATOM 1158 SG CYS A 153 39.178 57.419 53.592 1.00 13.86 S ATOM 747 SG CYS A 97 32.010 49.823 34.145 1.00 27.69 S ATOM 766 SG CYS A 100 35.538 49.934 34.447 1.00 18.56 S ATOM 793 SG CYS A 103 35.046 48.598 37.374 1.00 17.29 S ATOM 851 SG CYS A 111 33.725 51.995 36.289 1.00 24.14 S ATOM 2921 SG CYS B 43 75.575 61.223 24.891 1.00 31.49 S ATOM 3739 SG CYS B 153 74.222 57.419 26.208 1.00 13.75 S ATOM 3328 SG CYS B 97 81.390 49.823 45.655 1.00 26.93 S ATOM 3347 SG CYS B 100 77.862 49.934 45.353 1.00 18.55 S ATOM 3374 SG CYS B 103 78.354 48.598 42.426 1.00 17.28 S ATOM 3432 SG CYS B 111 79.675 51.995 43.511 1.00 23.84 S ATOM 5502 SG CYS C 43 75.575 22.777 54.909 1.00 31.13 S ATOM 6320 SG CYS C 153 74.222 26.581 53.592 1.00 13.83 S ATOM 5909 SG CYS C 97 81.390 34.177 34.144 1.00 27.76 S ATOM 5928 SG CYS C 100 77.862 34.067 34.447 1.00 18.86 S ATOM 5955 SG CYS C 103 78.354 35.402 37.374 1.00 17.65 S ATOM 6013 SG CYS C 111 79.675 32.005 36.289 1.00 24.21 S ATOM 8083 SG CYS D 43 37.825 22.777 24.891 1.00 30.86 S ATOM 8901 SG CYS D 153 39.178 26.581 26.208 1.00 13.46 S ATOM 8490 SG CYS D 97 32.010 34.177 45.656 1.00 27.10 S ATOM 8509 SG CYS D 100 35.538 34.067 45.353 1.00 18.70 S ATOM 8536 SG CYS D 103 35.046 35.402 42.426 1.00 17.32 S ATOM 8594 SG CYS D 111 33.725 32.005 43.511 1.00 24.09 S Time building chain proxies: 6.02, per 1000 atoms: 0.58 Number of scatterers: 10332 At special positions: 0 Unit cell: (114.45, 85.05, 80.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 8 29.99 S 56 16.00 O 1968 8.00 N 1752 7.00 C 6548 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS B 277 " distance=2.03 Simple disulfide: pdb=" SG CYS C 277 " - pdb=" SG CYS D 277 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.09 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 66 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 153 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 103 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 111 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 100 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 66 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 153 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 97 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 103 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 111 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 100 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 66 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 153 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 103 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 111 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 100 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 66 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 153 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 97 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 103 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 111 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 100 " Number of angles added : 24 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 20 sheets defined 34.6% alpha, 27.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 43 through 52 removed outlier: 3.740A pdb=" N LEU A 47 " --> pdb=" O CYS A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.555A pdb=" N ASN A 110 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.945A pdb=" N VAL A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 165 Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.696A pdb=" N LEU A 185 " --> pdb=" O GLY A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 214 Processing helix chain 'A' and resid 226 through 236 Processing helix chain 'A' and resid 248 through 256 removed outlier: 3.667A pdb=" N THR A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 287 Processing helix chain 'A' and resid 297 through 309 Processing helix chain 'A' and resid 323 through 325 No H-bonds generated for 'chain 'A' and resid 323 through 325' Processing helix chain 'A' and resid 326 through 335 removed outlier: 3.795A pdb=" N LYS A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 52 removed outlier: 3.740A pdb=" N LEU B 47 " --> pdb=" O CYS B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.555A pdb=" N ASN B 110 " --> pdb=" O ASN B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.945A pdb=" N VAL B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 165 Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.696A pdb=" N LEU B 185 " --> pdb=" O GLY B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 214 Processing helix chain 'B' and resid 226 through 236 Processing helix chain 'B' and resid 248 through 256 removed outlier: 3.667A pdb=" N THR B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 279 through 287 Processing helix chain 'B' and resid 297 through 309 Processing helix chain 'B' and resid 323 through 325 No H-bonds generated for 'chain 'B' and resid 323 through 325' Processing helix chain 'B' and resid 326 through 335 removed outlier: 3.795A pdb=" N LYS B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 52 removed outlier: 3.740A pdb=" N LEU C 47 " --> pdb=" O CYS C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 106 Processing helix chain 'C' and resid 107 through 111 removed outlier: 3.555A pdb=" N ASN C 110 " --> pdb=" O ASN C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 152 removed outlier: 3.945A pdb=" N VAL C 151 " --> pdb=" O GLU C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 153 through 165 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.696A pdb=" N LEU C 185 " --> pdb=" O GLY C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 214 Processing helix chain 'C' and resid 226 through 236 Processing helix chain 'C' and resid 248 through 256 removed outlier: 3.667A pdb=" N THR C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 287 Processing helix chain 'C' and resid 297 through 309 Processing helix chain 'C' and resid 323 through 325 No H-bonds generated for 'chain 'C' and resid 323 through 325' Processing helix chain 'C' and resid 326 through 335 removed outlier: 3.795A pdb=" N LYS C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 52 removed outlier: 3.740A pdb=" N LEU D 47 " --> pdb=" O CYS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 107 through 111 removed outlier: 3.555A pdb=" N ASN D 110 " --> pdb=" O ASN D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.945A pdb=" N VAL D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 165 Processing helix chain 'D' and resid 181 through 194 removed outlier: 3.696A pdb=" N LEU D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 214 Processing helix chain 'D' and resid 226 through 236 Processing helix chain 'D' and resid 248 through 256 removed outlier: 3.667A pdb=" N THR D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 287 Processing helix chain 'D' and resid 297 through 309 Processing helix chain 'D' and resid 323 through 325 No H-bonds generated for 'chain 'D' and resid 323 through 325' Processing helix chain 'D' and resid 326 through 335 removed outlier: 3.795A pdb=" N LYS D 334 " --> pdb=" O GLU D 330 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 10 Processing sheet with id=AA2, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU A 67 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER A 40 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA A 69 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU A 34 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET A 75 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU A 32 " --> pdb=" O MET A 75 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU A 67 " --> pdb=" O SER A 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER A 40 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA A 69 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU A 34 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET A 75 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU A 32 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR A 341 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 93 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 217 through 220 removed outlier: 6.792A pdb=" N VAL A 197 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE A 219 " --> pdb=" O VAL A 197 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY A 199 " --> pdb=" O ILE A 219 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL A 173 " --> pdb=" O LEU A 198 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE A 200 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE A 175 " --> pdb=" O ILE A 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP A 172 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 243 " --> pdb=" O TRP A 172 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA A 174 " --> pdb=" O ILE A 243 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA A 239 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN A 262 " --> pdb=" O ALA A 239 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY A 241 " --> pdb=" O ASN A 262 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR A 264 " --> pdb=" O GLY A 241 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE A 243 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL A 266 " --> pdb=" O ILE A 243 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 5 through 10 Processing sheet with id=AA7, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU B 67 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B 40 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA B 69 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 34 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET B 75 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU B 32 " --> pdb=" O MET B 75 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU B 67 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER B 40 " --> pdb=" O GLU B 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA B 69 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU B 34 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET B 75 " --> pdb=" O GLU B 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU B 32 " --> pdb=" O MET B 75 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR B 341 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 93 through 95 Processing sheet with id=AB1, first strand: chain 'B' and resid 217 through 220 removed outlier: 6.792A pdb=" N VAL B 197 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE B 219 " --> pdb=" O VAL B 197 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY B 199 " --> pdb=" O ILE B 219 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL B 173 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE B 200 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE B 175 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP B 172 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE B 243 " --> pdb=" O TRP B 172 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA B 174 " --> pdb=" O ILE B 243 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA B 239 " --> pdb=" O ARG B 260 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN B 262 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY B 241 " --> pdb=" O ASN B 262 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 264 " --> pdb=" O GLY B 241 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE B 243 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL B 266 " --> pdb=" O ILE B 243 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 10 Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU C 67 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER C 40 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA C 69 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU C 34 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET C 75 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU C 32 " --> pdb=" O MET C 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU C 67 " --> pdb=" O SER C 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER C 40 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA C 69 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU C 34 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET C 75 " --> pdb=" O GLU C 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU C 32 " --> pdb=" O MET C 75 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR C 341 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 93 through 95 Processing sheet with id=AB6, first strand: chain 'C' and resid 217 through 220 removed outlier: 6.792A pdb=" N VAL C 197 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE C 219 " --> pdb=" O VAL C 197 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY C 199 " --> pdb=" O ILE C 219 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL C 173 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE C 200 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE C 175 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP C 172 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE C 243 " --> pdb=" O TRP C 172 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA C 174 " --> pdb=" O ILE C 243 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA C 239 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN C 262 " --> pdb=" O ALA C 239 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY C 241 " --> pdb=" O ASN C 262 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR C 264 " --> pdb=" O GLY C 241 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE C 243 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL C 266 " --> pdb=" O ILE C 243 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 5 through 10 Processing sheet with id=AB8, first strand: chain 'D' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU D 67 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER D 40 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA D 69 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU D 34 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET D 75 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU D 32 " --> pdb=" O MET D 75 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 87 through 90 removed outlier: 6.559A pdb=" N GLU D 67 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER D 40 " --> pdb=" O GLU D 67 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ALA D 69 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N LEU D 34 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N MET D 75 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N GLU D 32 " --> pdb=" O MET D 75 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR D 341 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 93 through 95 Processing sheet with id=AC2, first strand: chain 'D' and resid 217 through 220 removed outlier: 6.792A pdb=" N VAL D 197 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ILE D 219 " --> pdb=" O VAL D 197 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N GLY D 199 " --> pdb=" O ILE D 219 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N VAL D 173 " --> pdb=" O LEU D 198 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N ILE D 200 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE D 175 " --> pdb=" O ILE D 200 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N TRP D 172 " --> pdb=" O GLY D 241 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE D 243 " --> pdb=" O TRP D 172 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ALA D 174 " --> pdb=" O ILE D 243 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ALA D 239 " --> pdb=" O ARG D 260 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N ASN D 262 " --> pdb=" O ALA D 239 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLY D 241 " --> pdb=" O ASN D 262 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR D 264 " --> pdb=" O GLY D 241 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N ILE D 243 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 266 " --> pdb=" O ILE D 243 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1188 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: 3.27 Time building geometry restraints manager: 4.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3376 1.34 - 1.46: 2076 1.46 - 1.58: 5008 1.58 - 1.70: 0 1.70 - 1.81: 80 Bond restraints: 10540 Sorted by residual: bond pdb=" CA SER B 96 " pdb=" CB SER B 96 " ideal model delta sigma weight residual 1.534 1.478 0.056 1.45e-02 4.76e+03 1.51e+01 bond pdb=" CA SER A 96 " pdb=" CB SER A 96 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.45e-02 4.76e+03 1.45e+01 bond pdb=" CA SER D 96 " pdb=" CB SER D 96 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.45e-02 4.76e+03 1.44e+01 bond pdb=" CA SER C 96 " pdb=" CB SER C 96 " ideal model delta sigma weight residual 1.534 1.479 0.055 1.45e-02 4.76e+03 1.44e+01 bond pdb=" N CYS C 100 " pdb=" CA CYS C 100 " ideal model delta sigma weight residual 1.453 1.485 -0.032 1.22e-02 6.72e+03 6.77e+00 ... (remaining 10535 not shown) Histogram of bond angle deviations from ideal: 99.65 - 106.52: 308 106.52 - 113.39: 5872 113.39 - 120.26: 3804 120.26 - 127.13: 4168 127.13 - 134.01: 136 Bond angle restraints: 14288 Sorted by residual: angle pdb=" N ALA B 99 " pdb=" CA ALA B 99 " pdb=" C ALA B 99 " ideal model delta sigma weight residual 114.64 107.21 7.43 1.52e+00 4.33e-01 2.39e+01 angle pdb=" N ALA C 99 " pdb=" CA ALA C 99 " pdb=" C ALA C 99 " ideal model delta sigma weight residual 114.64 107.22 7.42 1.52e+00 4.33e-01 2.39e+01 angle pdb=" N ALA D 99 " pdb=" CA ALA D 99 " pdb=" C ALA D 99 " ideal model delta sigma weight residual 114.64 107.22 7.42 1.52e+00 4.33e-01 2.39e+01 angle pdb=" N ALA A 99 " pdb=" CA ALA A 99 " pdb=" C ALA A 99 " ideal model delta sigma weight residual 114.64 107.22 7.42 1.52e+00 4.33e-01 2.38e+01 angle pdb=" CA CYS A 111 " pdb=" C CYS A 111 " pdb=" N PRO A 112 " ideal model delta sigma weight residual 118.87 122.80 -3.93 9.00e-01 1.23e+00 1.90e+01 ... (remaining 14283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 5420 17.18 - 34.37: 554 34.37 - 51.55: 148 51.55 - 68.73: 40 68.73 - 85.91: 16 Dihedral angle restraints: 6178 sinusoidal: 2314 harmonic: 3864 Sorted by residual: dihedral pdb=" CA TYR B 294 " pdb=" C TYR B 294 " pdb=" N VAL B 295 " pdb=" CA VAL B 295 " ideal model delta harmonic sigma weight residual 180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR D 294 " pdb=" C TYR D 294 " pdb=" N VAL D 295 " pdb=" CA VAL D 295 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA TYR A 294 " pdb=" C TYR A 294 " pdb=" N VAL A 295 " pdb=" CA VAL A 295 " ideal model delta harmonic sigma weight residual -180.00 -161.13 -18.87 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 6175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1112 0.052 - 0.104: 352 0.104 - 0.156: 116 0.156 - 0.208: 8 0.208 - 0.260: 4 Chirality restraints: 1592 Sorted by residual: chirality pdb=" CA MET D 168 " pdb=" N MET D 168 " pdb=" C MET D 168 " pdb=" CB MET D 168 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA MET A 168 " pdb=" N MET A 168 " pdb=" C MET A 168 " pdb=" CB MET A 168 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA MET C 168 " pdb=" N MET C 168 " pdb=" C MET C 168 " pdb=" CB MET C 168 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1589 not shown) Planarity restraints: 1844 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 325 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO D 326 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO D 326 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 326 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 325 " -0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO C 326 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO C 326 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 326 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 325 " 0.025 5.00e-02 4.00e+02 3.79e-02 2.30e+00 pdb=" N PRO B 326 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 326 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 326 " 0.019 5.00e-02 4.00e+02 ... (remaining 1841 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 68 2.57 - 3.15: 8456 3.15 - 3.73: 15853 3.73 - 4.32: 24945 4.32 - 4.90: 42082 Nonbonded interactions: 91404 Sorted by model distance: nonbonded pdb=" OE2 GLU C 67 " pdb="ZN ZN C 401 " model vdw 1.987 2.230 nonbonded pdb=" OE2 GLU A 67 " pdb="ZN ZN A 401 " model vdw 1.987 2.230 nonbonded pdb=" OE2 GLU B 67 " pdb="ZN ZN B 401 " model vdw 1.987 2.230 nonbonded pdb=" OE2 GLU D 67 " pdb="ZN ZN D 401 " model vdw 1.987 2.230 nonbonded pdb=" O CYS C 153 " pdb=" OG1 THR C 157 " model vdw 2.267 2.440 ... (remaining 91399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.800 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 33.100 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.011 0.062 10540 Z= 0.714 Angle : 0.799 7.429 14288 Z= 0.490 Chirality : 0.056 0.260 1592 Planarity : 0.004 0.038 1844 Dihedral : 15.993 85.911 3748 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 7.09 % Allowed : 15.67 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -4.00 (0.18), residues: 1380 helix: -2.41 (0.18), residues: 444 sheet: -2.99 (0.30), residues: 168 loop : -2.79 (0.18), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 50 HIS 0.004 0.001 HIS C 138 PHE 0.008 0.002 PHE A 221 TYR 0.020 0.003 TYR B 258 ARG 0.005 0.001 ARG D 298 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 96 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8756 (pp) REVERT: A 77 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7026 (mp0) REVERT: A 236 ASP cc_start: 0.7797 (t70) cc_final: 0.7375 (t0) REVERT: B 33 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8757 (pp) REVERT: B 77 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7018 (mp0) REVERT: B 236 ASP cc_start: 0.7791 (t70) cc_final: 0.7372 (t0) REVERT: C 33 LEU cc_start: 0.9152 (OUTLIER) cc_final: 0.8765 (pp) REVERT: C 77 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7015 (mp0) REVERT: C 236 ASP cc_start: 0.7795 (t70) cc_final: 0.7374 (t0) REVERT: D 33 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8763 (pp) REVERT: D 77 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: D 236 ASP cc_start: 0.7791 (t70) cc_final: 0.7373 (t0) outliers start: 76 outliers final: 40 residues processed: 160 average time/residue: 0.2547 time to fit residues: 57.4826 Evaluate side-chains 132 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 84 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 25 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 63 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 63 VAL Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 120 THR Chi-restraints excluded: chain D residue 176 SER Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 106 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 4.9990 chunk 123 optimal weight: 0.4980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS A 94 ASN ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 336 GLN B 44 HIS B 94 ASN ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 GLN C 44 HIS C 94 ASN ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 336 GLN D 44 HIS D 94 ASN ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 336 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 10540 Z= 0.183 Angle : 0.472 5.053 14288 Z= 0.245 Chirality : 0.044 0.134 1592 Planarity : 0.004 0.033 1844 Dihedral : 7.079 63.836 1552 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.36 % Allowed : 18.56 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -2.24 (0.21), residues: 1380 helix: -0.55 (0.22), residues: 460 sheet: -2.58 (0.27), residues: 224 loop : -1.70 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 50 HIS 0.002 0.001 HIS C 48 PHE 0.016 0.001 PHE A 210 TYR 0.015 0.001 TYR D 258 ARG 0.001 0.000 ARG A 298 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8809 (m-80) cc_final: 0.8085 (m-80) REVERT: A 44 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7332 (t-90) REVERT: A 86 ASP cc_start: 0.8090 (m-30) cc_final: 0.7876 (m-30) REVERT: A 193 MET cc_start: 0.9240 (mtp) cc_final: 0.8960 (mtp) REVERT: A 219 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8205 (mp) REVERT: A 236 ASP cc_start: 0.7749 (t70) cc_final: 0.7265 (t0) REVERT: B 39 TYR cc_start: 0.8808 (m-80) cc_final: 0.8085 (m-80) REVERT: B 44 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.7340 (t-90) REVERT: B 86 ASP cc_start: 0.8090 (m-30) cc_final: 0.7873 (m-30) REVERT: B 193 MET cc_start: 0.9238 (mtp) cc_final: 0.8958 (mtp) REVERT: B 219 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8205 (mp) REVERT: B 236 ASP cc_start: 0.7743 (t70) cc_final: 0.7259 (t0) REVERT: C 39 TYR cc_start: 0.8810 (m-80) cc_final: 0.8090 (m-80) REVERT: C 44 HIS cc_start: 0.7625 (OUTLIER) cc_final: 0.7337 (t-90) REVERT: C 86 ASP cc_start: 0.8092 (m-30) cc_final: 0.7880 (m-30) REVERT: C 193 MET cc_start: 0.9238 (mtp) cc_final: 0.8961 (mtp) REVERT: C 219 ILE cc_start: 0.8827 (OUTLIER) cc_final: 0.8206 (mp) REVERT: C 236 ASP cc_start: 0.7751 (t70) cc_final: 0.7267 (t0) REVERT: D 39 TYR cc_start: 0.8808 (m-80) cc_final: 0.8087 (m-80) REVERT: D 44 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.7333 (t-90) REVERT: D 86 ASP cc_start: 0.8095 (m-30) cc_final: 0.7875 (m-30) REVERT: D 193 MET cc_start: 0.9239 (mtp) cc_final: 0.8959 (mtp) REVERT: D 219 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8203 (mp) REVERT: D 236 ASP cc_start: 0.7745 (t70) cc_final: 0.7265 (t0) outliers start: 36 outliers final: 24 residues processed: 146 average time/residue: 0.2490 time to fit residues: 51.1802 Evaluate side-chains 130 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 98 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 0.3980 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 110 optimal weight: 0.1980 chunk 122 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 HIS ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 HIS ** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 44 HIS ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 HIS ** D 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 10540 Z= 0.159 Angle : 0.435 4.922 14288 Z= 0.226 Chirality : 0.043 0.132 1592 Planarity : 0.003 0.027 1844 Dihedral : 5.344 34.432 1508 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.92 % Allowed : 19.40 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.21 (0.22), residues: 1380 helix: 0.52 (0.24), residues: 460 sheet: -2.19 (0.29), residues: 224 loop : -1.18 (0.24), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 172 HIS 0.008 0.001 HIS C 44 PHE 0.013 0.001 PHE C 210 TYR 0.014 0.001 TYR D 258 ARG 0.001 0.000 ARG D 257 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 98 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8710 (m-80) cc_final: 0.7952 (m-80) REVERT: A 86 ASP cc_start: 0.8028 (m-30) cc_final: 0.7772 (m-30) REVERT: A 104 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7874 (mt-10) REVERT: A 219 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8298 (mp) REVERT: A 236 ASP cc_start: 0.7782 (t70) cc_final: 0.7275 (t0) REVERT: B 39 TYR cc_start: 0.8705 (m-80) cc_final: 0.7951 (m-80) REVERT: B 86 ASP cc_start: 0.8027 (m-30) cc_final: 0.7778 (m-30) REVERT: B 104 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7890 (mt-10) REVERT: B 219 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8305 (mp) REVERT: B 236 ASP cc_start: 0.7778 (t70) cc_final: 0.7276 (t0) REVERT: C 39 TYR cc_start: 0.8713 (m-80) cc_final: 0.7957 (m-80) REVERT: C 86 ASP cc_start: 0.8032 (m-30) cc_final: 0.7781 (m-30) REVERT: C 104 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7852 (mt-10) REVERT: C 219 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8301 (mp) REVERT: C 236 ASP cc_start: 0.7782 (t70) cc_final: 0.7279 (t0) REVERT: D 39 TYR cc_start: 0.8709 (m-80) cc_final: 0.7952 (m-80) REVERT: D 86 ASP cc_start: 0.8030 (m-30) cc_final: 0.7779 (m-30) REVERT: D 104 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7859 (mt-10) REVERT: D 219 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8303 (mp) REVERT: D 236 ASP cc_start: 0.7778 (t70) cc_final: 0.7277 (t0) outliers start: 42 outliers final: 32 residues processed: 136 average time/residue: 0.1724 time to fit residues: 36.7332 Evaluate side-chains 128 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 92 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 5.9990 chunk 93 optimal weight: 0.4980 chunk 64 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 109 optimal weight: 8.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 262 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10540 Z= 0.210 Angle : 0.437 4.996 14288 Z= 0.227 Chirality : 0.044 0.132 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.257 34.140 1508 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.10 % Allowed : 19.03 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.80 (0.23), residues: 1380 helix: 0.82 (0.24), residues: 460 sheet: -1.88 (0.31), residues: 224 loop : -0.93 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 92 HIS 0.001 0.000 HIS D 138 PHE 0.011 0.001 PHE D 210 TYR 0.016 0.001 TYR B 258 ARG 0.001 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 98 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8733 (m-80) cc_final: 0.8025 (m-80) REVERT: A 86 ASP cc_start: 0.8022 (m-30) cc_final: 0.7813 (m-30) REVERT: A 104 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 219 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8305 (mp) REVERT: A 236 ASP cc_start: 0.7837 (t70) cc_final: 0.7346 (t0) REVERT: B 39 TYR cc_start: 0.8733 (m-80) cc_final: 0.8028 (m-80) REVERT: B 86 ASP cc_start: 0.8013 (m-30) cc_final: 0.7807 (m-30) REVERT: B 104 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7871 (mt-10) REVERT: B 219 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8307 (mp) REVERT: B 236 ASP cc_start: 0.7828 (t70) cc_final: 0.7338 (t0) REVERT: C 39 TYR cc_start: 0.8736 (m-80) cc_final: 0.8031 (m-80) REVERT: C 86 ASP cc_start: 0.8014 (m-30) cc_final: 0.7808 (m-30) REVERT: C 104 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7853 (mt-10) REVERT: C 219 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8307 (mp) REVERT: C 236 ASP cc_start: 0.7835 (t70) cc_final: 0.7346 (t0) REVERT: D 39 TYR cc_start: 0.8737 (m-80) cc_final: 0.8029 (m-80) REVERT: D 86 ASP cc_start: 0.8015 (m-30) cc_final: 0.7805 (m-30) REVERT: D 104 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7850 (mt-10) REVERT: D 219 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8301 (mp) REVERT: D 236 ASP cc_start: 0.7831 (t70) cc_final: 0.7343 (t0) outliers start: 44 outliers final: 36 residues processed: 138 average time/residue: 0.1794 time to fit residues: 37.7958 Evaluate side-chains 134 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 94 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ASN Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 107 ASN Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 107 ASN Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 7.9990 chunk 1 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 117 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 ASN ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 36 ASN ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 10540 Z= 0.542 Angle : 0.597 6.738 14288 Z= 0.303 Chirality : 0.050 0.138 1592 Planarity : 0.004 0.026 1844 Dihedral : 6.090 36.374 1508 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.66 % Allowed : 20.34 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -1.16 (0.22), residues: 1380 helix: 0.26 (0.23), residues: 460 sheet: -1.76 (0.32), residues: 220 loop : -1.06 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 92 HIS 0.002 0.001 HIS B 138 PHE 0.008 0.002 PHE A 11 TYR 0.019 0.002 TYR B 258 ARG 0.003 0.001 ARG D 260 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 100 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8842 (m-80) cc_final: 0.8142 (m-80) REVERT: A 44 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7348 (t-90) REVERT: A 86 ASP cc_start: 0.8158 (m-30) cc_final: 0.7924 (m-30) REVERT: A 219 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 236 ASP cc_start: 0.7903 (t70) cc_final: 0.7356 (t0) REVERT: B 39 TYR cc_start: 0.8840 (m-80) cc_final: 0.8141 (m-80) REVERT: B 44 HIS cc_start: 0.7797 (OUTLIER) cc_final: 0.7363 (t-90) REVERT: B 86 ASP cc_start: 0.8151 (m-30) cc_final: 0.7920 (m-30) REVERT: B 193 MET cc_start: 0.9217 (mtp) cc_final: 0.8900 (mtp) REVERT: B 219 ILE cc_start: 0.8862 (OUTLIER) cc_final: 0.8293 (mp) REVERT: B 236 ASP cc_start: 0.7901 (t70) cc_final: 0.7354 (t0) REVERT: C 39 TYR cc_start: 0.8843 (m-80) cc_final: 0.8143 (m-80) REVERT: C 44 HIS cc_start: 0.7789 (OUTLIER) cc_final: 0.7355 (t-90) REVERT: C 86 ASP cc_start: 0.8152 (m-30) cc_final: 0.7923 (m-30) REVERT: C 219 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8292 (mp) REVERT: C 236 ASP cc_start: 0.7903 (t70) cc_final: 0.7358 (t0) REVERT: D 39 TYR cc_start: 0.8847 (m-80) cc_final: 0.8150 (m-80) REVERT: D 44 HIS cc_start: 0.7787 (OUTLIER) cc_final: 0.7356 (t-90) REVERT: D 86 ASP cc_start: 0.8152 (m-30) cc_final: 0.7919 (m-30) REVERT: D 193 MET cc_start: 0.9219 (mtp) cc_final: 0.8902 (mtp) REVERT: D 219 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8288 (mp) REVERT: D 236 ASP cc_start: 0.7899 (t70) cc_final: 0.7358 (t0) outliers start: 50 outliers final: 32 residues processed: 146 average time/residue: 0.2344 time to fit residues: 48.7855 Evaluate side-chains 140 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 100 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 109 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 10540 Z= 0.172 Angle : 0.445 4.905 14288 Z= 0.226 Chirality : 0.043 0.130 1592 Planarity : 0.003 0.024 1844 Dihedral : 5.325 34.183 1508 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.01 % Allowed : 20.43 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.55 (0.23), residues: 1380 helix: 0.90 (0.23), residues: 460 sheet: -1.48 (0.33), residues: 224 loop : -0.78 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 92 HIS 0.002 0.000 HIS B 121 PHE 0.013 0.001 PHE A 210 TYR 0.016 0.001 TYR C 258 ARG 0.001 0.000 ARG C 298 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 98 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8758 (m-80) cc_final: 0.8026 (m-80) REVERT: A 44 HIS cc_start: 0.7666 (OUTLIER) cc_final: 0.7269 (t-90) REVERT: A 86 ASP cc_start: 0.8027 (m-30) cc_final: 0.7779 (m-30) REVERT: A 104 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 219 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8300 (mp) REVERT: A 236 ASP cc_start: 0.7912 (t70) cc_final: 0.7333 (t0) REVERT: A 327 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.5312 (mp0) REVERT: B 39 TYR cc_start: 0.8757 (m-80) cc_final: 0.8028 (m-80) REVERT: B 44 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7281 (t-90) REVERT: B 86 ASP cc_start: 0.8017 (m-30) cc_final: 0.7772 (m-30) REVERT: B 104 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7898 (mt-10) REVERT: B 219 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8264 (mp) REVERT: B 236 ASP cc_start: 0.7902 (t70) cc_final: 0.7328 (t0) REVERT: B 327 GLU cc_start: 0.7139 (OUTLIER) cc_final: 0.5316 (mp0) REVERT: C 39 TYR cc_start: 0.8760 (m-80) cc_final: 0.8032 (m-80) REVERT: C 44 HIS cc_start: 0.7674 (OUTLIER) cc_final: 0.7274 (t-90) REVERT: C 86 ASP cc_start: 0.8023 (m-30) cc_final: 0.7774 (m-30) REVERT: C 104 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7875 (mt-10) REVERT: C 219 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8299 (mp) REVERT: C 236 ASP cc_start: 0.7911 (t70) cc_final: 0.7337 (t0) REVERT: C 327 GLU cc_start: 0.7140 (OUTLIER) cc_final: 0.5312 (mp0) REVERT: D 39 TYR cc_start: 0.8760 (m-80) cc_final: 0.8029 (m-80) REVERT: D 44 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7284 (t-90) REVERT: D 86 ASP cc_start: 0.8019 (m-30) cc_final: 0.7769 (m-30) REVERT: D 104 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7873 (mt-10) REVERT: D 219 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8292 (mp) REVERT: D 236 ASP cc_start: 0.7902 (t70) cc_final: 0.7334 (t0) outliers start: 43 outliers final: 32 residues processed: 141 average time/residue: 0.2114 time to fit residues: 43.1253 Evaluate side-chains 141 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 98 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 96 optimal weight: 0.0980 chunk 110 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10540 Z= 0.276 Angle : 0.476 5.190 14288 Z= 0.244 Chirality : 0.045 0.133 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.447 33.137 1508 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.48 % Allowed : 19.96 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.47 (0.23), residues: 1380 helix: 0.92 (0.23), residues: 460 sheet: -1.42 (0.34), residues: 224 loop : -0.69 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 92 HIS 0.002 0.000 HIS B 121 PHE 0.009 0.001 PHE A 210 TYR 0.016 0.001 TYR B 258 ARG 0.001 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 98 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8770 (m-80) cc_final: 0.8079 (m-80) REVERT: A 44 HIS cc_start: 0.7701 (OUTLIER) cc_final: 0.7312 (t-90) REVERT: A 86 ASP cc_start: 0.8047 (m-30) cc_final: 0.7774 (m-30) REVERT: A 219 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8315 (mp) REVERT: A 236 ASP cc_start: 0.7922 (t70) cc_final: 0.7359 (t0) REVERT: B 39 TYR cc_start: 0.8767 (m-80) cc_final: 0.8080 (m-80) REVERT: B 44 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7323 (t-90) REVERT: B 86 ASP cc_start: 0.8036 (m-30) cc_final: 0.7767 (m-30) REVERT: B 219 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 236 ASP cc_start: 0.7914 (t70) cc_final: 0.7350 (t0) REVERT: C 39 TYR cc_start: 0.8771 (m-80) cc_final: 0.8080 (m-80) REVERT: C 44 HIS cc_start: 0.7706 (OUTLIER) cc_final: 0.7320 (t-90) REVERT: C 86 ASP cc_start: 0.8041 (m-30) cc_final: 0.7771 (m-30) REVERT: C 219 ILE cc_start: 0.8861 (OUTLIER) cc_final: 0.8314 (mp) REVERT: C 236 ASP cc_start: 0.7924 (t70) cc_final: 0.7357 (t0) REVERT: D 39 TYR cc_start: 0.8771 (m-80) cc_final: 0.8079 (m-80) REVERT: D 44 HIS cc_start: 0.7708 (OUTLIER) cc_final: 0.7313 (t-90) REVERT: D 86 ASP cc_start: 0.8035 (m-30) cc_final: 0.7763 (m-30) REVERT: D 219 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8311 (mp) REVERT: D 236 ASP cc_start: 0.7916 (t70) cc_final: 0.7351 (t0) REVERT: D 327 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.5464 (mp0) outliers start: 48 outliers final: 37 residues processed: 145 average time/residue: 0.2338 time to fit residues: 48.5824 Evaluate side-chains 136 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 90 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 125 optimal weight: 0.8980 chunk 114 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10540 Z= 0.207 Angle : 0.449 4.972 14288 Z= 0.230 Chirality : 0.044 0.131 1592 Planarity : 0.003 0.022 1844 Dihedral : 5.292 33.999 1508 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 5.22 % Allowed : 19.96 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.28 (0.23), residues: 1380 helix: 1.13 (0.24), residues: 460 sheet: -1.30 (0.34), residues: 224 loop : -0.63 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 172 HIS 0.002 0.000 HIS C 121 PHE 0.011 0.001 PHE A 210 TYR 0.016 0.001 TYR C 258 ARG 0.001 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 93 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8754 (m-80) cc_final: 0.7991 (m-80) REVERT: A 44 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7294 (t-90) REVERT: A 86 ASP cc_start: 0.7995 (m-30) cc_final: 0.7733 (m-30) REVERT: A 104 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7906 (mt-10) REVERT: A 219 ILE cc_start: 0.8844 (OUTLIER) cc_final: 0.8296 (mp) REVERT: A 236 ASP cc_start: 0.7925 (t70) cc_final: 0.7339 (t0) REVERT: B 39 TYR cc_start: 0.8732 (m-80) cc_final: 0.7963 (m-80) REVERT: B 44 HIS cc_start: 0.7693 (OUTLIER) cc_final: 0.7305 (t-90) REVERT: B 86 ASP cc_start: 0.7984 (m-30) cc_final: 0.7725 (m-30) REVERT: B 104 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7902 (mt-10) REVERT: B 219 ILE cc_start: 0.8846 (OUTLIER) cc_final: 0.8296 (mp) REVERT: B 236 ASP cc_start: 0.7917 (t70) cc_final: 0.7334 (t0) REVERT: C 39 TYR cc_start: 0.8735 (m-80) cc_final: 0.7965 (m-80) REVERT: C 44 HIS cc_start: 0.7689 (OUTLIER) cc_final: 0.7303 (t-90) REVERT: C 86 ASP cc_start: 0.7987 (m-30) cc_final: 0.7728 (m-30) REVERT: C 219 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8282 (mp) REVERT: C 236 ASP cc_start: 0.7923 (t70) cc_final: 0.7337 (t0) REVERT: D 39 TYR cc_start: 0.8738 (m-80) cc_final: 0.7964 (m-80) REVERT: D 44 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.7295 (t-90) REVERT: D 86 ASP cc_start: 0.7984 (m-30) cc_final: 0.7724 (m-30) REVERT: D 104 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7886 (mt-10) REVERT: D 219 ILE cc_start: 0.8833 (OUTLIER) cc_final: 0.8277 (mp) REVERT: D 236 ASP cc_start: 0.7917 (t70) cc_final: 0.7343 (t0) REVERT: D 327 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.5394 (mp0) outliers start: 56 outliers final: 41 residues processed: 144 average time/residue: 0.2136 time to fit residues: 44.4550 Evaluate side-chains 143 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 93 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 95 optimal weight: 8.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10540 Z= 0.272 Angle : 0.471 5.185 14288 Z= 0.241 Chirality : 0.045 0.132 1592 Planarity : 0.003 0.022 1844 Dihedral : 5.397 33.032 1508 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.13 % Allowed : 20.06 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.36 (0.23), residues: 1380 helix: 1.03 (0.23), residues: 460 sheet: -1.34 (0.35), residues: 224 loop : -0.65 (0.26), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 92 HIS 0.002 0.000 HIS C 121 PHE 0.009 0.001 PHE A 210 TYR 0.017 0.001 TYR B 258 ARG 0.001 0.000 ARG B 257 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 94 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8757 (m-80) cc_final: 0.8059 (m-80) REVERT: A 44 HIS cc_start: 0.7721 (OUTLIER) cc_final: 0.7300 (t-90) REVERT: A 86 ASP cc_start: 0.8012 (m-30) cc_final: 0.7745 (m-30) REVERT: A 219 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8318 (mp) REVERT: A 236 ASP cc_start: 0.7939 (t70) cc_final: 0.7361 (t0) REVERT: B 39 TYR cc_start: 0.8757 (m-80) cc_final: 0.8062 (m-80) REVERT: B 44 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7315 (t-90) REVERT: B 86 ASP cc_start: 0.7999 (m-30) cc_final: 0.7736 (m-30) REVERT: B 219 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8308 (mp) REVERT: B 236 ASP cc_start: 0.7936 (t70) cc_final: 0.7355 (t0) REVERT: C 39 TYR cc_start: 0.8761 (m-80) cc_final: 0.8063 (m-80) REVERT: C 44 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.7309 (t-90) REVERT: C 86 ASP cc_start: 0.8001 (m-30) cc_final: 0.7738 (m-30) REVERT: C 219 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8301 (mp) REVERT: C 236 ASP cc_start: 0.7941 (t70) cc_final: 0.7354 (t0) REVERT: D 39 TYR cc_start: 0.8761 (m-80) cc_final: 0.8062 (m-80) REVERT: D 44 HIS cc_start: 0.7724 (OUTLIER) cc_final: 0.7303 (t-90) REVERT: D 86 ASP cc_start: 0.7997 (m-30) cc_final: 0.7733 (m-30) REVERT: D 219 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8297 (mp) REVERT: D 236 ASP cc_start: 0.7935 (t70) cc_final: 0.7348 (t0) REVERT: D 327 GLU cc_start: 0.7100 (OUTLIER) cc_final: 0.5422 (mp0) outliers start: 55 outliers final: 46 residues processed: 143 average time/residue: 0.2142 time to fit residues: 44.2366 Evaluate side-chains 149 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 94 time to evaluate : 1.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 GLU Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain B residue 19 GLU Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 19 GLU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain D residue 19 GLU Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 124 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 10540 Z= 0.416 Angle : 0.538 6.025 14288 Z= 0.275 Chirality : 0.048 0.135 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.781 33.574 1508 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.41 % Allowed : 19.78 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.62 (0.23), residues: 1380 helix: 0.72 (0.23), residues: 460 sheet: -1.34 (0.35), residues: 220 loop : -0.80 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 92 HIS 0.002 0.001 HIS B 138 PHE 0.007 0.001 PHE A 11 TYR 0.018 0.002 TYR C 258 ARG 0.001 0.000 ARG B 260 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 97 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 TYR cc_start: 0.8803 (m-80) cc_final: 0.8094 (m-80) REVERT: A 44 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7302 (t-90) REVERT: A 86 ASP cc_start: 0.8108 (m-30) cc_final: 0.7870 (m-30) REVERT: A 219 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8295 (mp) REVERT: A 236 ASP cc_start: 0.7926 (t70) cc_final: 0.7538 (t0) REVERT: A 327 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.5431 (mp0) REVERT: B 39 TYR cc_start: 0.8804 (m-80) cc_final: 0.8098 (m-80) REVERT: B 44 HIS cc_start: 0.7765 (OUTLIER) cc_final: 0.7317 (t-90) REVERT: B 86 ASP cc_start: 0.8098 (m-30) cc_final: 0.7844 (m-30) REVERT: B 219 ILE cc_start: 0.8843 (OUTLIER) cc_final: 0.8296 (mp) REVERT: B 236 ASP cc_start: 0.7920 (t70) cc_final: 0.7532 (t0) REVERT: B 327 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.5429 (mp0) REVERT: C 39 TYR cc_start: 0.8806 (m-80) cc_final: 0.8102 (m-80) REVERT: C 44 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7310 (t-90) REVERT: C 86 ASP cc_start: 0.8103 (m-30) cc_final: 0.7847 (m-30) REVERT: C 219 ILE cc_start: 0.8841 (OUTLIER) cc_final: 0.8291 (mp) REVERT: C 236 ASP cc_start: 0.7923 (t70) cc_final: 0.7531 (t0) REVERT: C 327 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.5429 (mp0) REVERT: D 39 TYR cc_start: 0.8808 (m-80) cc_final: 0.8099 (m-80) REVERT: D 44 HIS cc_start: 0.7759 (OUTLIER) cc_final: 0.7313 (t-90) REVERT: D 86 ASP cc_start: 0.8099 (m-30) cc_final: 0.7839 (m-30) REVERT: D 219 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8292 (mp) REVERT: D 236 ASP cc_start: 0.7919 (t70) cc_final: 0.7529 (t0) REVERT: D 327 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.5488 (mp0) outliers start: 58 outliers final: 42 residues processed: 150 average time/residue: 0.2218 time to fit residues: 47.3645 Evaluate side-chains 147 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 93 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 HIS Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 219 ILE Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 295 VAL Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 327 GLU Chi-restraints excluded: chain A residue 338 VAL Chi-restraints excluded: chain A residue 346 SER Chi-restraints excluded: chain B residue 44 HIS Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 197 VAL Chi-restraints excluded: chain B residue 219 ILE Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 295 VAL Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 314 LYS Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain B residue 327 GLU Chi-restraints excluded: chain B residue 338 VAL Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 197 VAL Chi-restraints excluded: chain C residue 219 ILE Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 295 VAL Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 314 LYS Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 346 SER Chi-restraints excluded: chain D residue 44 HIS Chi-restraints excluded: chain D residue 75 MET Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 197 VAL Chi-restraints excluded: chain D residue 219 ILE Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 295 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 314 LYS Chi-restraints excluded: chain D residue 323 SER Chi-restraints excluded: chain D residue 327 GLU Chi-restraints excluded: chain D residue 338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.130271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.105920 restraints weight = 9623.692| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 1.14 r_work: 0.2819 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 10540 Z= 0.155 Angle : 0.434 4.903 14288 Z= 0.222 Chirality : 0.043 0.129 1592 Planarity : 0.003 0.023 1844 Dihedral : 5.090 34.536 1508 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.29 % Allowed : 20.90 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 15.38 % 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: -0.21 (0.24), residues: 1380 helix: 1.22 (0.24), residues: 460 sheet: -1.20 (0.35), residues: 224 loop : -0.64 (0.25), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 50 HIS 0.002 0.000 HIS C 121 PHE 0.013 0.001 PHE A 210 TYR 0.016 0.001 TYR A 258 ARG 0.002 0.000 ARG B 298 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2072.82 seconds wall clock time: 38 minutes 42.05 seconds (2322.05 seconds total)