Starting phenix.real_space_refine on Tue Feb 13 22:25:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcp_29940/02_2024/8gcp_29940_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcp_29940/02_2024/8gcp_29940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcp_29940/02_2024/8gcp_29940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcp_29940/02_2024/8gcp_29940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcp_29940/02_2024/8gcp_29940_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gcp_29940/02_2024/8gcp_29940_updated.pdb" } resolution = 3.1 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= 0.002 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5047 2.51 5 N 1340 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "R ARG 212": "NH1" <-> "NH2" Residue "R ARG 316": "NH1" <-> "NH2" 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: 7921 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1548 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 54} Link IDs: {'PTRANS': 2, 'TRANS': 213} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 204 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 171 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'PHE%COO:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 7, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 107 Chain: "B" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2476 Classifications: {'peptide': 337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 362 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1614 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 127 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 6, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 97 Chain: "R" Number of atoms: 1896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1896 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 11, 'TRANS': 259} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 293 Unresolved non-hydrogen dihedrals: 189 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 122 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.48, per 1000 atoms: 0.57 Number of scatterers: 7921 At special positions: 0 Unit cell: (90.95, 119.85, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1477 8.00 N 1340 7.00 C 5047 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.05 Simple disulfide: pdb=" SG CYS R 92 " - pdb=" SG CYS R 170 " distance=2.05 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: 3.06 Conformation dependent library (CDL) restraints added in 1.7 seconds 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 30.2% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.54 Creating SS restraints... Processing helix chain 'A' and resid 7 through 30 Processing helix chain 'A' and resid 47 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 243 through 254 Processing helix chain 'A' and resid 271 through 280 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'A' and resid 332 through 340 Processing helix chain 'A' and resid 343 through 351 removed outlier: 3.587A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 23 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'R' and resid 23 through 44 removed outlier: 3.975A pdb=" N GLY R 34 " --> pdb=" O PHE R 30 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASN R 35 " --> pdb=" O GLY R 31 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU R 36 " --> pdb=" O VAL R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 53 through 81 Proline residue: R 74 - end of helix Processing helix chain 'R' and resid 90 through 114 removed outlier: 3.983A pdb=" N PHE R 97 " --> pdb=" O GLU R 93 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N PHE R 102 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N SER R 114 " --> pdb=" O ILE R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 122 removed outlier: 3.596A pdb=" N ILE R 121 " --> pdb=" O ARG R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 130 Processing helix chain 'R' and resid 135 through 156 removed outlier: 4.106A pdb=" N LEU R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) Proline residue: R 154 - end of helix Processing helix chain 'R' and resid 182 through 217 removed outlier: 3.576A pdb=" N LEU R 211 " --> pdb=" O CYS R 207 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG R 212 " --> pdb=" O GLY R 208 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET R 213 " --> pdb=" O ALA R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 271 through 297 removed outlier: 3.828A pdb=" N SER R 278 " --> pdb=" O LEU R 274 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LEU R 279 " --> pdb=" O ILE R 275 " (cutoff:3.500A) Proline residue: R 287 - end of helix Processing helix chain 'R' and resid 312 through 323 removed outlier: 3.769A pdb=" N SER R 319 " --> pdb=" O ILE R 315 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL R 320 " --> pdb=" O ARG R 316 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ASN R 321 " --> pdb=" O ILE R 317 " (cutoff:3.500A) Proline residue: R 322 - end of helix Processing helix chain 'R' and resid 326 through 329 No H-bonds generated for 'chain 'R' and resid 326 through 329' Processing sheet with id= A, first strand: chain 'A' and resid 34 through 37 removed outlier: 3.536A pdb=" N VAL A 34 " --> pdb=" O HIS A 195 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 222 through 225 removed outlier: 6.787A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.907A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.049A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 178 through 180 removed outlier: 3.543A pdb=" N CYS B 166 " --> pdb=" O PHE B 180 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 220 through 222 Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.762A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 284 through 288 Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.909A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 4 through 7 Processing sheet with id= K, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'E' and resid 226 through 228 removed outlier: 3.669A pdb=" N ILE E 189 " --> pdb=" O TRP E 176 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 330 hydrogen bonds defined for protein. 936 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: 2.40 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1310 1.31 - 1.44: 2213 1.44 - 1.57: 4472 1.57 - 1.70: 2 1.70 - 1.82: 79 Bond restraints: 8076 Sorted by residual: bond pdb=" C13 P2E R 501 " pdb=" C14 P2E R 501 " ideal model delta sigma weight residual 1.329 1.530 -0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C5 P2E R 501 " pdb=" C6 P2E R 501 " ideal model delta sigma weight residual 1.333 1.527 -0.194 2.00e-02 2.50e+03 9.39e+01 bond pdb=" C CYS R 59 " pdb=" N GLY R 60 " ideal model delta sigma weight residual 1.334 1.228 0.106 1.32e-02 5.74e+03 6.41e+01 bond pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 1.453 1.519 -0.066 1.31e-02 5.83e+03 2.57e+01 bond pdb=" CA VAL B 307 " pdb=" C VAL B 307 " ideal model delta sigma weight residual 1.523 1.462 0.061 1.27e-02 6.20e+03 2.33e+01 ... (remaining 8071 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.21: 196 106.21 - 113.34: 4361 113.34 - 120.48: 3306 120.48 - 127.61: 3095 127.61 - 134.75: 70 Bond angle restraints: 11028 Sorted by residual: angle pdb=" C GLN R 299 " pdb=" N PRO R 300 " pdb=" CA PRO R 300 " ideal model delta sigma weight residual 120.51 130.47 -9.96 1.26e+00 6.30e-01 6.25e+01 angle pdb=" N PHE R 217 " pdb=" CA PHE R 217 " pdb=" C PHE R 217 " ideal model delta sigma weight residual 112.90 123.12 -10.22 1.31e+00 5.83e-01 6.09e+01 angle pdb=" N SER R 307 " pdb=" CA SER R 307 " pdb=" C SER R 307 " ideal model delta sigma weight residual 112.92 122.34 -9.42 1.23e+00 6.61e-01 5.87e+01 angle pdb=" N LEU R 302 " pdb=" CA LEU R 302 " pdb=" C LEU R 302 " ideal model delta sigma weight residual 108.56 121.01 -12.45 1.74e+00 3.30e-01 5.12e+01 angle pdb=" N ALA C 56 " pdb=" CA ALA C 56 " pdb=" C ALA C 56 " ideal model delta sigma weight residual 112.38 121.07 -8.69 1.22e+00 6.72e-01 5.07e+01 ... (remaining 11023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4270 17.73 - 35.45: 370 35.45 - 53.18: 61 53.18 - 70.91: 5 70.91 - 88.63: 4 Dihedral angle restraints: 4710 sinusoidal: 1503 harmonic: 3207 Sorted by residual: dihedral pdb=" CA LEU A 268 " pdb=" C LEU A 268 " pdb=" N ASN A 269 " pdb=" CA ASN A 269 " ideal model delta harmonic sigma weight residual -180.00 -154.64 -25.36 0 5.00e+00 4.00e-02 2.57e+01 dihedral pdb=" C ALA C 56 " pdb=" N ALA C 56 " pdb=" CA ALA C 56 " pdb=" CB ALA C 56 " ideal model delta harmonic sigma weight residual -122.60 -133.80 11.20 0 2.50e+00 1.60e-01 2.01e+01 dihedral pdb=" CA CYS A 286 " pdb=" C CYS A 286 " pdb=" N TYR A 287 " pdb=" CA TYR A 287 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 ... (remaining 4707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 1225 0.120 - 0.240: 78 0.240 - 0.360: 13 0.360 - 0.480: 7 0.480 - 0.600: 1 Chirality restraints: 1324 Sorted by residual: chirality pdb=" CA ALA C 56 " pdb=" N ALA C 56 " pdb=" C ALA C 56 " pdb=" CB ALA C 56 " both_signs ideal model delta sigma weight residual False 2.48 1.88 0.60 2.00e-01 2.50e+01 9.00e+00 chirality pdb=" CA PHE R 217 " pdb=" N PHE R 217 " pdb=" C PHE R 217 " pdb=" CB PHE R 217 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CA MET E 192 " pdb=" N MET E 192 " pdb=" C MET E 192 " pdb=" CB MET E 192 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.12e+00 ... (remaining 1321 not shown) Planarity restraints: 1403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 501 " 0.153 2.00e-02 2.50e+03 3.20e-01 1.02e+03 pdb=" C5 P2E R 501 " -0.424 2.00e-02 2.50e+03 pdb=" C6 P2E R 501 " 0.427 2.00e-02 2.50e+03 pdb=" C7 P2E R 501 " -0.156 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 174 " -0.031 2.00e-02 2.50e+03 2.69e-02 1.80e+01 pdb=" CG TRP R 174 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP R 174 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP R 174 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP R 174 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP R 174 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 174 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 174 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 174 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP R 174 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR E 235 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.64e+01 pdb=" N PRO E 236 " -0.175 5.00e-02 4.00e+02 pdb=" CA PRO E 236 " 0.057 5.00e-02 4.00e+02 pdb=" CD PRO E 236 " 0.052 5.00e-02 4.00e+02 ... (remaining 1400 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1729 2.77 - 3.31: 6879 3.31 - 3.84: 12571 3.84 - 4.37: 14224 4.37 - 4.90: 25234 Nonbonded interactions: 60637 Sorted by model distance: nonbonded pdb=" OG1 THR R 64 " pdb=" OH TYR R 144 " model vdw 2.242 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.268 2.440 nonbonded pdb=" O THR E 243 " pdb=" CG2 THR E 243 " model vdw 2.294 3.460 nonbonded pdb=" OD1 ASP B 163 " pdb=" OG1 THR B 165 " model vdw 2.303 2.440 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.312 2.440 ... (remaining 60632 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: 0.660 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: 2.580 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.680 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 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 0.201 8076 Z= 0.717 Angle : 1.264 14.515 11028 Z= 0.724 Chirality : 0.077 0.600 1324 Planarity : 0.012 0.320 1403 Dihedral : 13.822 88.634 2632 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 0.67 % Allowed : 2.02 % Favored : 97.31 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.24), residues: 1086 helix: -1.49 (0.25), residues: 355 sheet: -0.16 (0.34), residues: 244 loop : -2.40 (0.25), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.072 0.004 TRP R 174 HIS 0.017 0.003 HIS B 311 PHE 0.029 0.003 PHE A 196 TYR 0.027 0.003 TYR B 105 ARG 0.009 0.001 ARG E 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 0.648 Fit side-chains REVERT: A 270 LYS cc_start: 0.7003 (pttm) cc_final: 0.6784 (pttm) REVERT: B 209 LYS cc_start: 0.8645 (mttm) cc_final: 0.7098 (mtmt) REVERT: B 228 ASP cc_start: 0.7436 (p0) cc_final: 0.7222 (p0) REVERT: E 83 MET cc_start: 0.6809 (mtm) cc_final: 0.6396 (mtm) REVERT: E 243 THR cc_start: 0.8296 (t) cc_final: 0.8002 (m) outliers start: 5 outliers final: 1 residues processed: 144 average time/residue: 0.2023 time to fit residues: 39.4991 Evaluate side-chains 124 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 123 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 chunk 45 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 0.4980 chunk 84 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 331 ASN B 220 GLN B 340 ASN C 59 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8076 Z= 0.202 Angle : 0.594 12.332 11028 Z= 0.306 Chirality : 0.042 0.148 1324 Planarity : 0.004 0.056 1403 Dihedral : 6.630 84.468 1202 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.48 % Allowed : 9.69 % Favored : 88.83 % 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: -1.30 (0.25), residues: 1086 helix: 0.28 (0.29), residues: 350 sheet: -0.26 (0.34), residues: 252 loop : -2.09 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 174 HIS 0.005 0.001 HIS R 214 PHE 0.014 0.002 PHE B 151 TYR 0.011 0.001 TYR B 105 ARG 0.004 0.000 ARG E 191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 150 time to evaluate : 0.837 Fit side-chains REVERT: A 38 LEU cc_start: 0.8610 (tp) cc_final: 0.8341 (tt) REVERT: A 207 GLU cc_start: 0.7111 (tt0) cc_final: 0.6860 (tt0) REVERT: B 209 LYS cc_start: 0.8612 (mttm) cc_final: 0.7109 (mtmt) outliers start: 11 outliers final: 5 residues processed: 152 average time/residue: 0.1925 time to fit residues: 40.2531 Evaluate side-chains 141 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 136 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain R residue 27 MET Chi-restraints excluded: chain R residue 110 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 0.0030 chunk 30 optimal weight: 0.7980 chunk 81 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 106 optimal weight: 0.0060 chunk 87 optimal weight: 0.0970 chunk 97 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 overall best weight: 0.2604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8076 Z= 0.125 Angle : 0.503 10.311 11028 Z= 0.259 Chirality : 0.040 0.131 1324 Planarity : 0.003 0.037 1403 Dihedral : 5.891 82.374 1202 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.75 % Allowed : 14.67 % Favored : 83.58 % 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: -0.70 (0.26), residues: 1086 helix: 0.92 (0.30), residues: 350 sheet: 0.23 (0.34), residues: 243 loop : -1.90 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.001 PHE E 29 TYR 0.009 0.001 TYR B 59 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 0.867 Fit side-chains REVERT: A 38 LEU cc_start: 0.8514 (tp) cc_final: 0.8291 (tt) REVERT: A 207 GLU cc_start: 0.6965 (tt0) cc_final: 0.6733 (tt0) REVERT: B 209 LYS cc_start: 0.8535 (mttm) cc_final: 0.7094 (mtmt) REVERT: B 268 ASN cc_start: 0.7142 (m110) cc_final: 0.6915 (m-40) outliers start: 13 outliers final: 7 residues processed: 143 average time/residue: 0.2143 time to fit residues: 41.3063 Evaluate side-chains 140 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 133 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 110 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 7.9990 chunk 73 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN B 220 GLN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8076 Z= 0.225 Angle : 0.550 8.787 11028 Z= 0.285 Chirality : 0.042 0.140 1324 Planarity : 0.003 0.039 1403 Dihedral : 5.873 81.006 1202 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.29 % Allowed : 16.55 % Favored : 81.16 % 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: -0.46 (0.26), residues: 1086 helix: 1.21 (0.30), residues: 357 sheet: 0.35 (0.35), residues: 238 loop : -1.86 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 174 HIS 0.005 0.001 HIS E 35 PHE 0.019 0.002 PHE E 29 TYR 0.016 0.001 TYR B 105 ARG 0.002 0.000 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 139 time to evaluate : 0.778 Fit side-chains REVERT: A 38 LEU cc_start: 0.8580 (tp) cc_final: 0.8278 (tt) REVERT: A 197 LYS cc_start: 0.7695 (ptpt) cc_final: 0.7426 (ptpt) REVERT: A 207 GLU cc_start: 0.7034 (tt0) cc_final: 0.6801 (tt0) REVERT: B 209 LYS cc_start: 0.8601 (mttm) cc_final: 0.7133 (mtmt) REVERT: B 268 ASN cc_start: 0.7152 (m110) cc_final: 0.6922 (m-40) outliers start: 17 outliers final: 12 residues processed: 143 average time/residue: 0.2029 time to fit residues: 39.4292 Evaluate side-chains 147 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 30.0000 chunk 59 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 77 optimal weight: 0.0170 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 72 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8076 Z= 0.157 Angle : 0.504 7.644 11028 Z= 0.258 Chirality : 0.040 0.138 1324 Planarity : 0.003 0.039 1403 Dihedral : 5.585 84.681 1202 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.69 % Allowed : 16.42 % Favored : 80.89 % 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: -0.23 (0.26), residues: 1086 helix: 1.43 (0.30), residues: 357 sheet: 0.51 (0.34), residues: 248 loop : -1.82 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.020 0.001 PHE E 29 TYR 0.010 0.001 TYR R 94 ARG 0.004 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 141 time to evaluate : 0.815 Fit side-chains REVERT: A 38 LEU cc_start: 0.8536 (tp) cc_final: 0.8208 (tt) REVERT: A 197 LYS cc_start: 0.7654 (ptpt) cc_final: 0.7432 (ptpt) REVERT: A 207 GLU cc_start: 0.6948 (tt0) cc_final: 0.6681 (tt0) REVERT: B 209 LYS cc_start: 0.8532 (mttm) cc_final: 0.7169 (mtmt) REVERT: B 268 ASN cc_start: 0.7144 (m110) cc_final: 0.6920 (m-40) outliers start: 20 outliers final: 11 residues processed: 147 average time/residue: 0.1787 time to fit residues: 36.3130 Evaluate side-chains 150 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 2.9990 chunk 94 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 chunk 104 optimal weight: 50.0000 chunk 86 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 34 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8076 Z= 0.202 Angle : 0.523 7.934 11028 Z= 0.271 Chirality : 0.041 0.156 1324 Planarity : 0.003 0.037 1403 Dihedral : 5.590 88.956 1200 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.83 % Allowed : 17.90 % Favored : 79.27 % 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: -0.11 (0.27), residues: 1086 helix: 1.57 (0.30), residues: 357 sheet: 0.61 (0.35), residues: 248 loop : -1.80 (0.26), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.021 0.002 PHE E 29 TYR 0.011 0.001 TYR B 105 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 137 time to evaluate : 0.782 Fit side-chains REVERT: A 38 LEU cc_start: 0.8551 (tp) cc_final: 0.8244 (tt) REVERT: A 207 GLU cc_start: 0.6979 (tt0) cc_final: 0.6699 (tt0) REVERT: B 209 LYS cc_start: 0.8553 (mttm) cc_final: 0.7153 (mtmt) REVERT: B 268 ASN cc_start: 0.7159 (m110) cc_final: 0.6927 (m-40) REVERT: R 108 SER cc_start: 0.7721 (m) cc_final: 0.7491 (m) outliers start: 21 outliers final: 12 residues processed: 145 average time/residue: 0.1913 time to fit residues: 37.8147 Evaluate side-chains 152 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 30.0000 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 340 ASN R 147 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8076 Z= 0.194 Angle : 0.527 9.352 11028 Z= 0.271 Chirality : 0.041 0.144 1324 Planarity : 0.003 0.037 1403 Dihedral : 5.429 87.367 1200 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.96 % Allowed : 18.03 % Favored : 79.00 % 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: -0.03 (0.27), residues: 1086 helix: 1.66 (0.30), residues: 358 sheet: 0.67 (0.35), residues: 248 loop : -1.79 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.022 0.001 PHE E 29 TYR 0.009 0.001 TYR B 105 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 139 time to evaluate : 0.821 Fit side-chains REVERT: A 38 LEU cc_start: 0.8530 (tp) cc_final: 0.8204 (tt) REVERT: A 207 GLU cc_start: 0.6945 (tt0) cc_final: 0.6690 (tt0) REVERT: A 225 VAL cc_start: 0.7843 (t) cc_final: 0.7624 (t) REVERT: B 209 LYS cc_start: 0.8540 (mttm) cc_final: 0.7150 (mtmt) REVERT: B 268 ASN cc_start: 0.7161 (m110) cc_final: 0.6930 (m-40) REVERT: R 108 SER cc_start: 0.7735 (m) cc_final: 0.7498 (m) outliers start: 22 outliers final: 16 residues processed: 146 average time/residue: 0.1876 time to fit residues: 38.0039 Evaluate side-chains 154 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 138 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 70 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 81 optimal weight: 8.9990 chunk 94 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7160 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8076 Z= 0.231 Angle : 0.548 8.980 11028 Z= 0.283 Chirality : 0.042 0.151 1324 Planarity : 0.003 0.037 1403 Dihedral : 5.369 82.229 1200 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.69 % Allowed : 19.11 % Favored : 78.20 % 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: -0.02 (0.26), residues: 1086 helix: 1.67 (0.30), residues: 358 sheet: 0.59 (0.34), residues: 252 loop : -1.74 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.005 0.001 HIS E 35 PHE 0.022 0.002 PHE E 29 TYR 0.011 0.001 TYR B 105 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.826 Fit side-chains REVERT: A 38 LEU cc_start: 0.8560 (tp) cc_final: 0.8253 (tt) REVERT: A 207 GLU cc_start: 0.6982 (tt0) cc_final: 0.6728 (tt0) REVERT: A 225 VAL cc_start: 0.7877 (t) cc_final: 0.7667 (t) REVERT: B 209 LYS cc_start: 0.8569 (mttm) cc_final: 0.7171 (mtmt) REVERT: B 268 ASN cc_start: 0.7171 (m110) cc_final: 0.6945 (m-40) REVERT: R 27 MET cc_start: 0.4940 (mtt) cc_final: 0.4726 (ttt) REVERT: R 108 SER cc_start: 0.7726 (m) cc_final: 0.7474 (m) outliers start: 20 outliers final: 17 residues processed: 143 average time/residue: 0.1987 time to fit residues: 38.7189 Evaluate side-chains 152 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 135 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 0.2980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8076 Z= 0.355 Angle : 0.616 9.256 11028 Z= 0.321 Chirality : 0.045 0.171 1324 Planarity : 0.004 0.039 1403 Dihedral : 5.587 75.427 1200 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.83 % Allowed : 19.78 % Favored : 77.39 % 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: -0.18 (0.26), residues: 1086 helix: 1.56 (0.29), residues: 359 sheet: 0.52 (0.34), residues: 253 loop : -1.89 (0.26), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP R 174 HIS 0.006 0.002 HIS E 167 PHE 0.023 0.002 PHE E 29 TYR 0.016 0.002 TYR B 105 ARG 0.005 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 138 time to evaluate : 0.869 Fit side-chains REVERT: A 38 LEU cc_start: 0.8568 (tp) cc_final: 0.8262 (tt) REVERT: A 207 GLU cc_start: 0.6998 (tt0) cc_final: 0.6753 (tt0) REVERT: A 225 VAL cc_start: 0.7931 (t) cc_final: 0.7724 (t) REVERT: B 209 LYS cc_start: 0.8614 (mttm) cc_final: 0.7200 (mtmt) REVERT: R 27 MET cc_start: 0.5002 (mtt) cc_final: 0.4744 (ttt) REVERT: R 108 SER cc_start: 0.7658 (m) cc_final: 0.7405 (m) outliers start: 21 outliers final: 15 residues processed: 145 average time/residue: 0.1865 time to fit residues: 37.1774 Evaluate side-chains 150 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 135 time to evaluate : 0.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 213 MET Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 107 optimal weight: 0.0980 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 322 HIS ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 220 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8076 Z= 0.176 Angle : 0.527 8.829 11028 Z= 0.272 Chirality : 0.041 0.158 1324 Planarity : 0.003 0.038 1403 Dihedral : 5.092 69.007 1200 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.29 % Allowed : 20.19 % Favored : 77.52 % 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: 0.07 (0.27), residues: 1086 helix: 1.76 (0.30), residues: 359 sheet: 0.63 (0.35), residues: 252 loop : -1.72 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 169 HIS 0.005 0.001 HIS E 35 PHE 0.023 0.001 PHE E 29 TYR 0.009 0.001 TYR R 94 ARG 0.004 0.000 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2172 Ramachandran restraints generated. 1086 Oldfield, 0 Emsley, 1086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.778 Fit side-chains REVERT: A 207 GLU cc_start: 0.6940 (tt0) cc_final: 0.6719 (tt0) REVERT: B 209 LYS cc_start: 0.8543 (mttm) cc_final: 0.7150 (mtmt) REVERT: R 27 MET cc_start: 0.4993 (mtt) cc_final: 0.4781 (ttt) REVERT: R 108 SER cc_start: 0.7727 (m) cc_final: 0.7472 (m) outliers start: 17 outliers final: 16 residues processed: 145 average time/residue: 0.2129 time to fit residues: 41.8037 Evaluate side-chains 155 residues out of total 949 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 139 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 197 LYS Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain R residue 21 VAL Chi-restraints excluded: chain R residue 175 THR Chi-restraints excluded: chain R residue 218 MET Chi-restraints excluded: chain R residue 280 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.0370 chunk 85 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 0.0670 chunk 15 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.169870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.135964 restraints weight = 10936.129| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.06 r_work: 0.3439 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8076 Z= 0.160 Angle : 0.513 9.425 11028 Z= 0.263 Chirality : 0.041 0.151 1324 Planarity : 0.003 0.037 1403 Dihedral : 4.825 60.481 1200 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.29 % Allowed : 20.73 % Favored : 76.99 % 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: 0.25 (0.27), residues: 1086 helix: 2.07 (0.30), residues: 352 sheet: 0.71 (0.34), residues: 248 loop : -1.67 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.005 0.001 HIS E 35 PHE 0.024 0.001 PHE E 29 TYR 0.011 0.001 TYR E 173 ARG 0.004 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2093.53 seconds wall clock time: 38 minutes 31.60 seconds (2311.60 seconds total)