Starting phenix.real_space_refine on Wed Feb 14 10:47:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td3_25822/02_2024/7td3_25822_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td3_25822/02_2024/7td3_25822.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td3_25822/02_2024/7td3_25822_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td3_25822/02_2024/7td3_25822_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td3_25822/02_2024/7td3_25822_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td3_25822/02_2024/7td3_25822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td3_25822/02_2024/7td3_25822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td3_25822/02_2024/7td3_25822_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7td3_25822/02_2024/7td3_25822_updated.pdb" } resolution = 3.0 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= 0.975 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2072 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 53 5.16 5 C 4503 2.51 5 N 1193 2.21 5 O 1285 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 228": "OD1" <-> "OD2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 298": "OD1" <-> "OD2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "A TYR 320": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "R TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 225": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 229": "NH1" <-> "NH2" Residue "R ARG 231": "NH1" <-> "NH2" Residue "R ARG 233": "NH1" <-> "NH2" Residue "R PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 238": "NH1" <-> "NH2" Residue "R PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7035 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 2556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2556 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 36 Chain: "A" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1759 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "G" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 405 Classifications: {'peptide': 56} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 51} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Chain: "R" Number of atoms: 2315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2315 Unusual residues: {'NAG': 1, 'S1P': 1} Classifications: {'peptide': 292, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 6, 'TRANS': 285, None: 2} Not linked: pdbres="ILE R 323 " pdbres="S1P R 401 " Not linked: pdbres="S1P R 401 " pdbres="NAG R 402 " Chain breaks: 2 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 64 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 4.37, per 1000 atoms: 0.62 Number of scatterers: 7035 At special positions: 0 Unit cell: (93.138, 95.304, 132.126, 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) S 53 16.00 P 1 15.00 O 1285 8.00 N 1193 7.00 C 4503 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 191 " distance=2.03 Simple disulfide: pdb=" SG CYS R 282 " - pdb=" SG CYS R 287 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG R 402 " - " ASN R 30 " Time building additional restraints: 2.68 Conformation dependent library (CDL) restraints added in 1.3 seconds 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 8 sheets defined 42.2% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'B' and resid 4 through 25 removed outlier: 4.257A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'A' and resid 8 through 32 removed outlier: 4.106A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 53 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 227 through 231 removed outlier: 4.053A pdb=" N ASP A 231 " --> pdb=" O SER A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 271 through 279 removed outlier: 4.194A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 309 Processing helix chain 'A' and resid 331 through 351 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'R' and resid 22 through 31 removed outlier: 3.768A pdb=" N VAL R 26 " --> pdb=" O TYR R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 71 Processing helix chain 'R' and resid 74 through 76 No H-bonds generated for 'chain 'R' and resid 74 through 76' Processing helix chain 'R' and resid 79 through 104 Processing helix chain 'R' and resid 106 through 111 removed outlier: 3.536A pdb=" N THR R 109 " --> pdb=" O GLY R 106 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N TYR R 110 " --> pdb=" O ALA R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 148 removed outlier: 3.786A pdb=" N MET R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 157 through 175 removed outlier: 4.000A pdb=" N ILE R 164 " --> pdb=" O LEU R 160 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA R 166 " --> pdb=" O LEU R 162 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 234 removed outlier: 3.772A pdb=" N ARG R 234 " --> pdb=" O THR R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 281 removed outlier: 3.511A pdb=" N LEU R 255 " --> pdb=" O SER R 251 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS R 268 " --> pdb=" O VAL R 264 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 289 through 291 No H-bonds generated for 'chain 'R' and resid 289 through 291' Processing helix chain 'R' and resid 294 through 313 removed outlier: 3.638A pdb=" N VAL R 298 " --> pdb=" O GLU R 294 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 318 through 322 Processing sheet with id= A, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.945A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.655A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.703A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.978A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.827A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 307 through 309 removed outlier: 4.145A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.522A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 319 through 323 removed outlier: 6.369A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N HIS A 195 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N LEU A 36 " --> pdb=" O HIS A 195 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N LYS A 197 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N LEU A 38 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE A 199 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N GLY A 40 " --> pdb=" O PHE A 199 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 2.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.30: 1124 1.30 - 1.43: 1871 1.43 - 1.56: 4096 1.56 - 1.69: 1 1.69 - 1.83: 75 Bond restraints: 7167 Sorted by residual: bond pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " ideal model delta sigma weight residual 1.661 1.811 -0.150 2.00e-02 2.50e+03 5.62e+01 bond pdb=" C THR R 145 " pdb=" O THR R 145 " ideal model delta sigma weight residual 1.236 1.164 0.072 1.15e-02 7.56e+03 3.93e+01 bond pdb=" C MET R 146 " pdb=" O MET R 146 " ideal model delta sigma weight residual 1.237 1.164 0.073 1.17e-02 7.31e+03 3.84e+01 bond pdb=" CA SER R 192 " pdb=" CB SER R 192 " ideal model delta sigma weight residual 1.530 1.451 0.078 1.48e-02 4.57e+03 2.81e+01 bond pdb=" C PRO R 79 " pdb=" O PRO R 79 " ideal model delta sigma weight residual 1.237 1.171 0.066 1.26e-02 6.30e+03 2.75e+01 ... (remaining 7162 not shown) Histogram of bond angle deviations from ideal: 94.91 - 102.78: 33 102.78 - 110.64: 2379 110.64 - 118.51: 3309 118.51 - 126.38: 3898 126.38 - 134.24: 98 Bond angle restraints: 9717 Sorted by residual: angle pdb=" C PHE R 65 " pdb=" CA PHE R 65 " pdb=" CB PHE R 65 " ideal model delta sigma weight residual 110.88 100.63 10.25 1.57e+00 4.06e-01 4.26e+01 angle pdb=" C THR R 145 " pdb=" CA THR R 145 " pdb=" CB THR R 145 " ideal model delta sigma weight residual 110.88 101.56 9.32 1.57e+00 4.06e-01 3.53e+01 angle pdb=" CA THR R 193 " pdb=" CB THR R 193 " pdb=" OG1 THR R 193 " ideal model delta sigma weight residual 109.60 100.98 8.62 1.50e+00 4.44e-01 3.30e+01 angle pdb=" CA THR R 145 " pdb=" CB THR R 145 " pdb=" OG1 THR R 145 " ideal model delta sigma weight residual 109.60 101.33 8.27 1.50e+00 4.44e-01 3.04e+01 angle pdb=" O1 S1P R 401 " pdb=" P22 S1P R 401 " pdb=" O25 S1P R 401 " ideal model delta sigma weight residual 109.48 94.91 14.57 3.00e+00 1.11e-01 2.36e+01 ... (remaining 9712 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4008 17.97 - 35.95: 202 35.95 - 53.92: 43 53.92 - 71.89: 11 71.89 - 89.86: 5 Dihedral angle restraints: 4269 sinusoidal: 1613 harmonic: 2656 Sorted by residual: dihedral pdb=" CB CYS R 282 " pdb=" SG CYS R 282 " pdb=" SG CYS R 287 " pdb=" CB CYS R 287 " ideal model delta sinusoidal sigma weight residual -86.00 -147.71 61.71 1 1.00e+01 1.00e-02 5.05e+01 dihedral pdb=" C PHE R 65 " pdb=" N PHE R 65 " pdb=" CA PHE R 65 " pdb=" CB PHE R 65 " ideal model delta harmonic sigma weight residual -122.60 -110.13 -12.47 0 2.50e+00 1.60e-01 2.49e+01 dihedral pdb=" C CYS A 351 " pdb=" N CYS A 351 " pdb=" CA CYS A 351 " pdb=" CB CYS A 351 " ideal model delta harmonic sigma weight residual -122.60 -110.75 -11.85 0 2.50e+00 1.60e-01 2.25e+01 ... (remaining 4266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1041 0.077 - 0.153: 83 0.153 - 0.230: 14 0.230 - 0.306: 6 0.306 - 0.383: 5 Chirality restraints: 1149 Sorted by residual: chirality pdb=" CA MET R 149 " pdb=" N MET R 149 " pdb=" C MET R 149 " pdb=" CB MET R 149 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CA ASN R 157 " pdb=" N ASN R 157 " pdb=" C ASN R 157 " pdb=" CB ASN R 157 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA LYS R 150 " pdb=" N LYS R 150 " pdb=" C LYS R 150 " pdb=" CB LYS R 150 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.61e+00 ... (remaining 1146 not shown) Planarity restraints: 1209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 73 " 0.018 2.00e-02 2.50e+03 3.77e-02 1.42e+01 pdb=" C THR R 73 " -0.065 2.00e-02 2.50e+03 pdb=" O THR R 73 " 0.024 2.00e-02 2.50e+03 pdb=" N LYS R 74 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG R 159 " -0.018 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C ARG R 159 " 0.063 2.00e-02 2.50e+03 pdb=" O ARG R 159 " -0.023 2.00e-02 2.50e+03 pdb=" N LEU R 160 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 402 " -0.040 2.00e-02 2.50e+03 3.20e-02 1.28e+01 pdb=" C7 NAG R 402 " 0.010 2.00e-02 2.50e+03 pdb=" C8 NAG R 402 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG R 402 " 0.049 2.00e-02 2.50e+03 pdb=" O7 NAG R 402 " 0.011 2.00e-02 2.50e+03 ... (remaining 1206 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 66 2.63 - 3.20: 6329 3.20 - 3.76: 10495 3.76 - 4.33: 15435 4.33 - 4.90: 25367 Nonbonded interactions: 57692 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.059 2.440 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.193 2.440 nonbonded pdb=" O VAL R 96 " pdb=" OG1 THR R 99 " model vdw 2.334 2.440 nonbonded pdb=" O CYS A 254 " pdb=" NZ LYS A 317 " model vdw 2.336 2.520 nonbonded pdb=" OD1 ASP A 251 " pdb=" ND2 ASN A 255 " model vdw 2.337 2.520 ... (remaining 57687 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 3.930 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 23.610 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.150 7167 Z= 0.443 Angle : 0.794 14.569 9717 Z= 0.497 Chirality : 0.055 0.383 1149 Planarity : 0.005 0.041 1208 Dihedral : 12.221 89.864 2539 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.81 % Allowed : 6.10 % Favored : 93.09 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.27), residues: 895 helix: 1.02 (0.27), residues: 386 sheet: -0.51 (0.37), residues: 168 loop : -1.71 (0.29), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 71 HIS 0.004 0.001 HIS B 54 PHE 0.013 0.002 PHE R 65 TYR 0.009 0.001 TYR R 81 ARG 0.007 0.001 ARG R 159 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 197 time to evaluate : 0.884 Fit side-chains REVERT: B 22 ARG cc_start: 0.6830 (mtt180) cc_final: 0.6267 (mpt-90) REVERT: B 175 GLN cc_start: 0.7942 (mm-40) cc_final: 0.7696 (mm110) REVERT: B 197 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7556 (mmm-85) REVERT: B 234 PHE cc_start: 0.9383 (OUTLIER) cc_final: 0.8798 (m-80) REVERT: B 251 ARG cc_start: 0.8553 (mtt-85) cc_final: 0.8232 (mtt-85) REVERT: B 325 MET cc_start: 0.8307 (mmt) cc_final: 0.8032 (mmt) REVERT: B 333 ASP cc_start: 0.8959 (p0) cc_final: 0.8633 (p0) REVERT: A 25 GLU cc_start: 0.7029 (mt-10) cc_final: 0.6818 (mt-10) REVERT: A 29 LYS cc_start: 0.8410 (ttpp) cc_final: 0.8141 (tttp) REVERT: A 32 ARG cc_start: 0.8189 (mtm-85) cc_final: 0.7908 (mtm-85) REVERT: A 242 ARG cc_start: 0.7583 (ttm170) cc_final: 0.7336 (ttm-80) REVERT: A 298 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7201 (tt0) REVERT: A 345 LYS cc_start: 0.8145 (tttt) cc_final: 0.7231 (mttp) REVERT: A 349 LYS cc_start: 0.8464 (mtpt) cc_final: 0.8002 (mtmm) REVERT: G 52 THR cc_start: 0.7643 (m) cc_final: 0.7102 (p) outliers start: 6 outliers final: 2 residues processed: 200 average time/residue: 1.2319 time to fit residues: 260.0527 Evaluate side-chains 153 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 149 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain R residue 148 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 0.3980 chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.0170 chunk 80 optimal weight: 0.8980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 HIS ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 HIS R 199 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7167 Z= 0.174 Angle : 0.481 5.797 9717 Z= 0.261 Chirality : 0.042 0.141 1149 Planarity : 0.004 0.046 1208 Dihedral : 7.112 77.551 1024 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.93 % Allowed : 12.74 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.28), residues: 895 helix: 1.99 (0.27), residues: 383 sheet: -0.31 (0.37), residues: 170 loop : -1.51 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.000 HIS B 54 PHE 0.014 0.001 PHE R 58 TYR 0.011 0.001 TYR A 287 ARG 0.004 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 0.910 Fit side-chains REVERT: B 146 LEU cc_start: 0.9138 (tp) cc_final: 0.8823 (tp) REVERT: B 228 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8500 (m-30) REVERT: B 234 PHE cc_start: 0.9341 (OUTLIER) cc_final: 0.8756 (m-80) REVERT: B 268 ASN cc_start: 0.7687 (t0) cc_final: 0.7403 (t0) REVERT: B 281 SER cc_start: 0.9403 (OUTLIER) cc_final: 0.9186 (p) REVERT: B 333 ASP cc_start: 0.8916 (p0) cc_final: 0.8622 (p0) REVERT: A 25 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6786 (mt-10) REVERT: A 29 LYS cc_start: 0.8410 (ttpp) cc_final: 0.8175 (tttp) REVERT: A 32 ARG cc_start: 0.8172 (mtm-85) cc_final: 0.7882 (mtm-85) REVERT: A 248 LYS cc_start: 0.7872 (mtpp) cc_final: 0.7387 (mtpt) REVERT: A 298 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: A 345 LYS cc_start: 0.8121 (tttt) cc_final: 0.7233 (mptt) REVERT: A 349 LYS cc_start: 0.8367 (mtpt) cc_final: 0.7934 (mtmm) REVERT: R 78 ARG cc_start: 0.7802 (mtp180) cc_final: 0.7597 (mtp85) REVERT: R 153 ASN cc_start: 0.6007 (m-40) cc_final: 0.5780 (m110) outliers start: 29 outliers final: 9 residues processed: 184 average time/residue: 1.1924 time to fit residues: 231.0990 Evaluate side-chains 171 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 158 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 211 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 44 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 87 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 64 optimal weight: 0.0670 chunk 79 optimal weight: 0.5980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7167 Z= 0.175 Angle : 0.456 5.854 9717 Z= 0.249 Chirality : 0.041 0.181 1149 Planarity : 0.003 0.046 1208 Dihedral : 6.473 76.111 1020 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.88 % Allowed : 14.36 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.28), residues: 895 helix: 2.29 (0.27), residues: 384 sheet: -0.26 (0.37), residues: 172 loop : -1.41 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.017 0.001 PHE R 58 TYR 0.010 0.001 TYR R 225 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 161 time to evaluate : 0.749 Fit side-chains REVERT: B 146 LEU cc_start: 0.9122 (tp) cc_final: 0.8803 (tp) REVERT: B 234 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8736 (m-80) REVERT: B 268 ASN cc_start: 0.7758 (t0) cc_final: 0.7405 (t0) REVERT: A 25 GLU cc_start: 0.7036 (mt-10) cc_final: 0.6606 (mt-10) REVERT: A 29 LYS cc_start: 0.8360 (ttpp) cc_final: 0.8143 (tttp) REVERT: A 32 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7986 (mtm-85) REVERT: A 242 ARG cc_start: 0.7567 (ttm170) cc_final: 0.7319 (ttm-80) REVERT: A 248 LYS cc_start: 0.7907 (mtpp) cc_final: 0.7419 (mtpt) REVERT: A 298 GLU cc_start: 0.7518 (tt0) cc_final: 0.7251 (tt0) REVERT: A 345 LYS cc_start: 0.8124 (tttt) cc_final: 0.7240 (mptt) REVERT: A 349 LYS cc_start: 0.8391 (mtpt) cc_final: 0.7944 (mtmm) REVERT: G 38 MET cc_start: 0.7708 (ttp) cc_final: 0.7336 (ttp) REVERT: R 153 ASN cc_start: 0.6091 (m-40) cc_final: 0.5848 (m110) REVERT: R 233 ARG cc_start: 0.7182 (OUTLIER) cc_final: 0.6531 (mtt-85) outliers start: 36 outliers final: 17 residues processed: 179 average time/residue: 1.1531 time to fit residues: 217.4852 Evaluate side-chains 165 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 146 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 211 THR Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 60 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 0.3980 chunk 54 optimal weight: 0.2980 chunk 81 optimal weight: 0.0970 chunk 86 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 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 0.031 7167 Z= 0.141 Angle : 0.431 6.352 9717 Z= 0.233 Chirality : 0.040 0.170 1149 Planarity : 0.003 0.045 1208 Dihedral : 5.658 70.956 1017 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 4.34 % Allowed : 16.80 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.28), residues: 895 helix: 2.39 (0.27), residues: 390 sheet: -0.17 (0.38), residues: 172 loop : -1.37 (0.30), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.001 0.000 HIS B 183 PHE 0.017 0.001 PHE R 58 TYR 0.011 0.001 TYR R 225 ARG 0.003 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 157 time to evaluate : 0.784 Fit side-chains REVERT: B 146 LEU cc_start: 0.9101 (tp) cc_final: 0.8792 (tp) REVERT: B 234 PHE cc_start: 0.9344 (OUTLIER) cc_final: 0.8733 (m-80) REVERT: B 268 ASN cc_start: 0.7899 (t0) cc_final: 0.7512 (t0) REVERT: A 25 GLU cc_start: 0.7005 (mt-10) cc_final: 0.6579 (mt-10) REVERT: A 29 LYS cc_start: 0.8329 (ttpp) cc_final: 0.8106 (tttp) REVERT: A 32 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.7994 (mtm-85) REVERT: A 242 ARG cc_start: 0.7506 (ttm170) cc_final: 0.7153 (ttm-80) REVERT: A 248 LYS cc_start: 0.7951 (mtpp) cc_final: 0.7486 (mtpt) REVERT: A 298 GLU cc_start: 0.7546 (tt0) cc_final: 0.7245 (tt0) REVERT: A 345 LYS cc_start: 0.8098 (tttt) cc_final: 0.7236 (mptt) REVERT: A 349 LYS cc_start: 0.8361 (mtpt) cc_final: 0.7904 (mtmm) REVERT: G 38 MET cc_start: 0.7639 (ttp) cc_final: 0.7254 (ttp) REVERT: R 153 ASN cc_start: 0.5988 (m-40) cc_final: 0.5730 (m110) REVERT: R 233 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6608 (mtt-85) outliers start: 32 outliers final: 16 residues processed: 171 average time/residue: 1.2255 time to fit residues: 220.4001 Evaluate side-chains 172 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 154 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 284 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 1 optimal weight: 3.9990 chunk 64 optimal weight: 0.2980 chunk 35 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 7167 Z= 0.244 Angle : 0.473 5.566 9717 Z= 0.258 Chirality : 0.042 0.170 1149 Planarity : 0.004 0.048 1208 Dihedral : 5.723 67.547 1017 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.20 % Allowed : 17.48 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.28), residues: 895 helix: 2.46 (0.27), residues: 381 sheet: -0.18 (0.38), residues: 174 loop : -1.24 (0.30), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 54 PHE 0.020 0.002 PHE R 58 TYR 0.013 0.001 TYR R 225 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 0.781 Fit side-chains REVERT: B 146 LEU cc_start: 0.9132 (tp) cc_final: 0.8815 (tp) REVERT: B 234 PHE cc_start: 0.9343 (OUTLIER) cc_final: 0.8788 (m-80) REVERT: B 268 ASN cc_start: 0.7925 (t0) cc_final: 0.7535 (t0) REVERT: A 25 GLU cc_start: 0.7062 (mt-10) cc_final: 0.6634 (mt-10) REVERT: A 29 LYS cc_start: 0.8393 (ttpp) cc_final: 0.8157 (tttp) REVERT: A 32 ARG cc_start: 0.8246 (mtm-85) cc_final: 0.8010 (mtm-85) REVERT: A 232 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8119 (mm) REVERT: A 242 ARG cc_start: 0.7517 (ttm170) cc_final: 0.7158 (ttm-80) REVERT: A 248 LYS cc_start: 0.7948 (mtpp) cc_final: 0.7484 (mtpt) REVERT: A 270 LYS cc_start: 0.8322 (mmtt) cc_final: 0.8017 (mmtm) REVERT: A 298 GLU cc_start: 0.7600 (tt0) cc_final: 0.7314 (tt0) REVERT: A 308 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7522 (mt-10) REVERT: A 345 LYS cc_start: 0.8110 (tttt) cc_final: 0.7242 (mptt) REVERT: A 349 LYS cc_start: 0.8364 (mtpt) cc_final: 0.7939 (mtmm) REVERT: G 38 MET cc_start: 0.7749 (ttp) cc_final: 0.7361 (ttp) REVERT: G 51 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7878 (mp) REVERT: R 153 ASN cc_start: 0.6006 (m-40) cc_final: 0.5748 (m110) REVERT: R 233 ARG cc_start: 0.7296 (OUTLIER) cc_final: 0.6700 (mtt-85) outliers start: 31 outliers final: 17 residues processed: 168 average time/residue: 1.1359 time to fit residues: 201.2045 Evaluate side-chains 171 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 150 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 86 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7167 Z= 0.186 Angle : 0.447 5.749 9717 Z= 0.243 Chirality : 0.041 0.162 1149 Planarity : 0.003 0.046 1208 Dihedral : 5.548 67.854 1017 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.61 % Allowed : 17.89 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.28), residues: 895 helix: 2.58 (0.27), residues: 382 sheet: -0.05 (0.38), residues: 171 loop : -1.23 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.019 0.001 PHE R 58 TYR 0.014 0.001 TYR R 225 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 157 time to evaluate : 0.847 Fit side-chains REVERT: B 146 LEU cc_start: 0.9119 (tp) cc_final: 0.8817 (tp) REVERT: B 234 PHE cc_start: 0.9328 (OUTLIER) cc_final: 0.8767 (m-80) REVERT: B 268 ASN cc_start: 0.7963 (t0) cc_final: 0.7600 (t0) REVERT: A 25 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6635 (mt-10) REVERT: A 29 LYS cc_start: 0.8388 (ttpp) cc_final: 0.8152 (tttp) REVERT: A 32 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.8005 (mtm-85) REVERT: A 232 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8181 (mm) REVERT: A 242 ARG cc_start: 0.7487 (ttm170) cc_final: 0.7158 (ttm-80) REVERT: A 248 LYS cc_start: 0.7965 (mtpp) cc_final: 0.7501 (mtpt) REVERT: A 270 LYS cc_start: 0.8304 (mmtt) cc_final: 0.8009 (mmtm) REVERT: A 298 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.7274 (tt0) REVERT: A 345 LYS cc_start: 0.8106 (tttt) cc_final: 0.7237 (mptt) REVERT: A 349 LYS cc_start: 0.8354 (mtpt) cc_final: 0.7917 (mtmm) REVERT: G 38 MET cc_start: 0.7737 (ttp) cc_final: 0.7355 (ttp) REVERT: R 153 ASN cc_start: 0.5981 (m-40) cc_final: 0.5708 (m110) REVERT: R 233 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6708 (mtt-85) outliers start: 34 outliers final: 20 residues processed: 173 average time/residue: 1.1586 time to fit residues: 211.3249 Evaluate side-chains 174 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 284 VAL Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 39 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 36 ASN ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7167 Z= 0.191 Angle : 0.454 6.213 9717 Z= 0.247 Chirality : 0.041 0.163 1149 Planarity : 0.003 0.048 1208 Dihedral : 5.488 64.855 1017 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.20 % Allowed : 18.70 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.28), residues: 895 helix: 2.58 (0.27), residues: 382 sheet: 0.00 (0.38), residues: 176 loop : -1.23 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS A 188 PHE 0.019 0.001 PHE R 58 TYR 0.015 0.001 TYR R 225 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 0.827 Fit side-chains REVERT: B 146 LEU cc_start: 0.9128 (tp) cc_final: 0.8822 (tp) REVERT: B 175 GLN cc_start: 0.7666 (mm110) cc_final: 0.7373 (mm110) REVERT: B 234 PHE cc_start: 0.9318 (OUTLIER) cc_final: 0.8687 (m-80) REVERT: B 237 ASN cc_start: 0.8845 (p0) cc_final: 0.8624 (p0) REVERT: B 268 ASN cc_start: 0.7978 (t0) cc_final: 0.7625 (t0) REVERT: A 25 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6633 (mt-10) REVERT: A 29 LYS cc_start: 0.8392 (ttpp) cc_final: 0.8158 (tttp) REVERT: A 32 ARG cc_start: 0.8293 (mtm-85) cc_final: 0.8032 (mtm-85) REVERT: A 232 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8156 (mm) REVERT: A 242 ARG cc_start: 0.7467 (ttm170) cc_final: 0.7159 (ttm-80) REVERT: A 248 LYS cc_start: 0.7921 (mtpp) cc_final: 0.7461 (mtpt) REVERT: A 270 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7992 (mmtm) REVERT: A 298 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.7295 (tt0) REVERT: A 308 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7760 (mt-10) REVERT: A 345 LYS cc_start: 0.8105 (tttt) cc_final: 0.7238 (mptt) REVERT: A 349 LYS cc_start: 0.8351 (mtpt) cc_final: 0.7912 (mtmm) REVERT: G 38 MET cc_start: 0.7781 (ttp) cc_final: 0.7411 (ttp) REVERT: R 153 ASN cc_start: 0.5973 (m-40) cc_final: 0.5711 (m110) REVERT: R 233 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6728 (mtt-85) outliers start: 31 outliers final: 22 residues processed: 173 average time/residue: 1.1862 time to fit residues: 216.0230 Evaluate side-chains 182 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 156 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 67 optimal weight: 0.5980 chunk 78 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7167 Z= 0.191 Angle : 0.451 5.785 9717 Z= 0.246 Chirality : 0.041 0.162 1149 Planarity : 0.003 0.047 1208 Dihedral : 5.445 62.972 1017 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.61 % Allowed : 18.43 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.28), residues: 895 helix: 2.58 (0.27), residues: 384 sheet: 0.03 (0.38), residues: 176 loop : -1.20 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.021 0.001 PHE R 58 TYR 0.015 0.001 TYR R 225 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 154 time to evaluate : 0.851 Fit side-chains REVERT: B 146 LEU cc_start: 0.9150 (tp) cc_final: 0.8842 (tp) REVERT: B 175 GLN cc_start: 0.7696 (mm110) cc_final: 0.7402 (mm110) REVERT: B 234 PHE cc_start: 0.9308 (OUTLIER) cc_final: 0.8696 (m-80) REVERT: B 268 ASN cc_start: 0.8013 (t0) cc_final: 0.7660 (t0) REVERT: A 20 ASP cc_start: 0.7829 (m-30) cc_final: 0.7451 (m-30) REVERT: A 25 GLU cc_start: 0.7052 (mt-10) cc_final: 0.6635 (mt-10) REVERT: A 29 LYS cc_start: 0.8393 (ttpp) cc_final: 0.8162 (tttp) REVERT: A 32 ARG cc_start: 0.8313 (mtm-85) cc_final: 0.8066 (mtm-85) REVERT: A 232 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.8152 (mm) REVERT: A 242 ARG cc_start: 0.7435 (ttm170) cc_final: 0.7148 (ttm-80) REVERT: A 248 LYS cc_start: 0.7954 (mtpp) cc_final: 0.7499 (mtpt) REVERT: A 298 GLU cc_start: 0.7533 (OUTLIER) cc_final: 0.7279 (tt0) REVERT: A 345 LYS cc_start: 0.8099 (tttt) cc_final: 0.7242 (mptt) REVERT: A 349 LYS cc_start: 0.8344 (mtpt) cc_final: 0.7913 (mtmm) REVERT: G 51 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7913 (mp) REVERT: R 153 ASN cc_start: 0.5970 (m-40) cc_final: 0.5688 (m110) REVERT: R 233 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6756 (mtt-85) outliers start: 34 outliers final: 23 residues processed: 171 average time/residue: 1.2011 time to fit residues: 216.5456 Evaluate side-chains 181 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 153 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 271 LYS Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 34 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 0.0040 chunk 58 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7167 Z= 0.190 Angle : 0.453 5.748 9717 Z= 0.247 Chirality : 0.041 0.161 1149 Planarity : 0.003 0.047 1208 Dihedral : 5.395 60.293 1017 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.61 % Allowed : 18.29 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.28), residues: 895 helix: 2.67 (0.27), residues: 382 sheet: 0.05 (0.38), residues: 176 loop : -1.17 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.019 0.001 PHE R 58 TYR 0.015 0.001 TYR R 225 ARG 0.002 0.000 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 151 time to evaluate : 0.842 Fit side-chains REVERT: B 76 ASP cc_start: 0.8695 (p0) cc_final: 0.8322 (p0) REVERT: B 146 LEU cc_start: 0.9148 (tp) cc_final: 0.8839 (tp) REVERT: B 234 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8709 (m-80) REVERT: B 268 ASN cc_start: 0.7985 (t0) cc_final: 0.7645 (t0) REVERT: A 25 GLU cc_start: 0.7053 (mt-10) cc_final: 0.6632 (mt-10) REVERT: A 29 LYS cc_start: 0.8397 (ttpp) cc_final: 0.8176 (tttp) REVERT: A 32 ARG cc_start: 0.8315 (mtm-85) cc_final: 0.8065 (mtm-85) REVERT: A 51 LYS cc_start: 0.8135 (ttpt) cc_final: 0.7861 (ttmm) REVERT: A 232 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8155 (mm) REVERT: A 248 LYS cc_start: 0.7956 (mtpp) cc_final: 0.7501 (mtpt) REVERT: A 298 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7288 (tt0) REVERT: A 308 GLU cc_start: 0.8028 (mt-10) cc_final: 0.7744 (mt-10) REVERT: A 345 LYS cc_start: 0.8098 (tttt) cc_final: 0.7234 (mptt) REVERT: A 349 LYS cc_start: 0.8347 (mtpt) cc_final: 0.7907 (mtmm) REVERT: G 51 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7932 (mp) REVERT: R 153 ASN cc_start: 0.5961 (m-40) cc_final: 0.5667 (m110) REVERT: R 233 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6727 (mtt-85) outliers start: 34 outliers final: 23 residues processed: 167 average time/residue: 1.1570 time to fit residues: 203.4630 Evaluate side-chains 178 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 150 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 180 MET Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 213 LEU Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 88 optimal weight: 0.6980 chunk 81 optimal weight: 0.0020 chunk 70 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 43 optimal weight: 6.9990 chunk 56 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7167 Z= 0.150 Angle : 0.443 5.851 9717 Z= 0.240 Chirality : 0.041 0.159 1149 Planarity : 0.003 0.045 1208 Dihedral : 5.222 58.006 1017 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.79 % Allowed : 19.38 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.28), residues: 895 helix: 2.72 (0.26), residues: 384 sheet: 0.10 (0.38), residues: 176 loop : -1.13 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.001 0.000 HIS B 225 PHE 0.018 0.001 PHE R 58 TYR 0.015 0.001 TYR R 225 ARG 0.002 0.000 ARG B 214 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1790 Ramachandran restraints generated. 895 Oldfield, 0 Emsley, 895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 159 time to evaluate : 0.831 Fit side-chains REVERT: B 146 LEU cc_start: 0.9131 (tp) cc_final: 0.8809 (tp) REVERT: B 234 PHE cc_start: 0.9283 (OUTLIER) cc_final: 0.8721 (m-80) REVERT: B 268 ASN cc_start: 0.7981 (t0) cc_final: 0.7663 (t0) REVERT: A 20 ASP cc_start: 0.7803 (m-30) cc_final: 0.7431 (m-30) REVERT: A 25 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6656 (mt-10) REVERT: A 29 LYS cc_start: 0.8337 (ttpp) cc_final: 0.8129 (tttp) REVERT: A 32 ARG cc_start: 0.8297 (mtm-85) cc_final: 0.8010 (mtm-85) REVERT: A 51 LYS cc_start: 0.8030 (ttpt) cc_final: 0.7807 (ttmm) REVERT: A 232 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8146 (mm) REVERT: A 248 LYS cc_start: 0.7955 (mtpp) cc_final: 0.7503 (mtpt) REVERT: A 270 LYS cc_start: 0.8254 (mmtt) cc_final: 0.7986 (mmtm) REVERT: A 298 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6959 (tt0) REVERT: A 308 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7706 (mt-10) REVERT: A 345 LYS cc_start: 0.8084 (tttt) cc_final: 0.7216 (mptt) REVERT: A 349 LYS cc_start: 0.8313 (mtpt) cc_final: 0.7876 (mtmm) REVERT: G 51 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7997 (mp) REVERT: R 153 ASN cc_start: 0.5889 (m-40) cc_final: 0.5563 (m110) REVERT: R 233 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6665 (mtt-85) outliers start: 28 outliers final: 18 residues processed: 171 average time/residue: 1.1662 time to fit residues: 210.1557 Evaluate side-chains 181 residues out of total 788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 158 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain A residue 232 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 151 LEU Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain R residue 186 SER Chi-restraints excluded: chain R residue 233 ARG Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 19 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 overall best weight: 0.5838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.135063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.103772 restraints weight = 8574.513| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.12 r_work: 0.2875 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7167 Z= 0.189 Angle : 0.457 5.758 9717 Z= 0.249 Chirality : 0.041 0.185 1149 Planarity : 0.003 0.047 1208 Dihedral : 5.249 57.121 1017 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.52 % Allowed : 20.19 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.28), residues: 895 helix: 2.67 (0.26), residues: 384 sheet: 0.12 (0.38), residues: 176 loop : -1.14 (0.30), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.018 0.001 PHE R 58 TYR 0.015 0.001 TYR R 225 ARG 0.002 0.000 ARG B 214 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3726.78 seconds wall clock time: 66 minutes 42.83 seconds (4002.83 seconds total)