Starting phenix.real_space_refine on Sat Apr 6 23:39:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/04_2024/8jln_36401_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/04_2024/8jln_36401.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/04_2024/8jln_36401_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/04_2024/8jln_36401_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/04_2024/8jln_36401_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/04_2024/8jln_36401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/04_2024/8jln_36401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/04_2024/8jln_36401_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/04_2024/8jln_36401_updated.pdb" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 68 5.16 5 C 5814 2.51 5 N 1560 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 21": "OE1" <-> "OE2" Residue "A GLU 50": "OE1" <-> "OE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "B TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 86": "OE1" <-> "OE2" Residue "R GLU 93": "OE1" <-> "OE2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R GLU 169": "OE1" <-> "OE2" Residue "R GLU 170": "OE1" <-> "OE2" Residue "R GLU 219": "OE1" <-> "OE2" Residue "Y GLU 42": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9117 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1972 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2322 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 1 Chain: "S" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1767 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.41, per 1000 atoms: 0.59 Number of scatterers: 9117 At special positions: 0 Unit cell: (107.95, 118.15, 130.9, 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) I 1 52.95 S 68 16.00 O 1674 8.00 N 1560 7.00 C 5814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.15 Conformation dependent library (CDL) restraints added in 1.7 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 33.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 Creating SS restraints... Processing helix chain 'A' and resid 14 through 39 removed outlier: 4.396A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.111A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 49 Processing helix chain 'R' and resid 57 through 75 Processing helix chain 'R' and resid 77 through 83 removed outlier: 3.930A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 126 removed outlier: 4.014A pdb=" N HIS R 99 " --> pdb=" O CYS R 96 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N THR R 100 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU R 106 " --> pdb=" O ASP R 103 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N CYS R 126 " --> pdb=" O TYR R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 159 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 176 Processing helix chain 'R' and resid 179 through 181 No H-bonds generated for 'chain 'R' and resid 179 through 181' Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 231 Processing helix chain 'R' and resid 248 through 276 removed outlier: 4.439A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 283 through 304 removed outlier: 3.559A pdb=" N ILE R 290 " --> pdb=" O ASN R 286 " (cutoff:3.500A) Proline residue: R 301 - end of helix removed outlier: 3.814A pdb=" N TYR R 304 " --> pdb=" O ASN R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 309 through 317 Processing helix chain 'S' and resid 29 through 31 No H-bonds generated for 'chain 'S' and resid 29 through 31' Processing helix chain 'Y' and resid 7 through 25 Processing helix chain 'Y' and resid 30 through 44 Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.876A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.056A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.822A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.903A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 158 through 160 removed outlier: 3.563A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 191 removed outlier: 6.810A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 7.108A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 296 through 298 removed outlier: 3.991A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.854A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.769A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'S' and resid 3 through 8 removed outlier: 3.573A pdb=" N MET S 83 " --> pdb=" O ARG S 18 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'S' and resid 92 through 99 removed outlier: 5.237A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ALA S 40 " --> pdb=" O LEU S 45 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N LEU S 45 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'S' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'S' and resid 174 through 176 373 hydrogen bonds defined for protein. 1023 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: 2.43 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 3889 1.40 - 1.58: 5330 1.58 - 1.76: 0 1.76 - 1.93: 102 1.93 - 2.11: 1 Bond restraints: 9322 Sorted by residual: bond pdb=" N ASP R 103 " pdb=" CA ASP R 103 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.61e+00 bond pdb=" C ASP B 38 " pdb=" N PRO B 39 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.25e-02 6.40e+03 1.42e+00 bond pdb=" C THR R 102 " pdb=" N ASP R 103 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.34e-02 5.57e+03 1.20e+00 bond pdb=" CG MET Y 21 " pdb=" SD MET Y 21 " ideal model delta sigma weight residual 1.803 1.778 0.025 2.50e-02 1.60e+03 1.01e+00 bond pdb=" CA ILE A 288 " pdb=" CB ILE A 288 " ideal model delta sigma weight residual 1.540 1.527 0.013 1.36e-02 5.41e+03 8.94e-01 ... (remaining 9317 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.06: 170 106.06 - 113.08: 4973 113.08 - 120.10: 3286 120.10 - 127.12: 4090 127.12 - 134.13: 100 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C11 UJF R 401 " pdb=" C12 UJF R 401 " pdb=" I01 UJF R 401 " ideal model delta sigma weight residual 105.19 119.07 -13.88 3.00e+00 1.11e-01 2.14e+01 angle pdb=" C LYS Y 20 " pdb=" N MET Y 21 " pdb=" CA MET Y 21 " ideal model delta sigma weight residual 121.58 114.90 6.68 1.95e+00 2.63e-01 1.18e+01 angle pdb=" N VAL R 176 " pdb=" CA VAL R 176 " pdb=" C VAL R 176 " ideal model delta sigma weight residual 112.98 108.92 4.06 1.25e+00 6.40e-01 1.06e+01 angle pdb=" N VAL R 94 " pdb=" CA VAL R 94 " pdb=" C VAL R 94 " ideal model delta sigma weight residual 111.81 109.08 2.73 8.60e-01 1.35e+00 1.01e+01 angle pdb=" C ASP R 103 " pdb=" N ILE R 104 " pdb=" CA ILE R 104 " ideal model delta sigma weight residual 120.55 125.28 -4.73 1.60e+00 3.91e-01 8.74e+00 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 4949 18.14 - 36.29: 478 36.29 - 54.43: 79 54.43 - 72.57: 10 72.57 - 90.72: 7 Dihedral angle restraints: 5523 sinusoidal: 2172 harmonic: 3351 Sorted by residual: dihedral pdb=" CA GLY A 225 " pdb=" C GLY A 225 " pdb=" N ALA A 226 " pdb=" CA ALA A 226 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5520 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 911 0.034 - 0.068: 326 0.068 - 0.102: 116 0.102 - 0.136: 46 0.136 - 0.170: 4 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA MET Y 21 " pdb=" N MET Y 21 " pdb=" C MET Y 21 " pdb=" CB MET Y 21 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CB ILE R 280 " pdb=" CA ILE R 280 " pdb=" CG1 ILE R 280 " pdb=" CG2 ILE R 280 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB THR A 350 " pdb=" CA THR A 350 " pdb=" OG1 THR A 350 " pdb=" CG2 THR A 350 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1400 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 310 " -0.014 2.00e-02 2.50e+03 1.55e-02 6.03e+00 pdb=" CG TRP R 310 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP R 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP R 310 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 310 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 310 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 310 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 310 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 310 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO S 151 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO S 107 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " -0.024 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1446 2.76 - 3.31: 8931 3.31 - 3.86: 15089 3.86 - 4.41: 17517 4.41 - 4.96: 30929 Nonbonded interactions: 73912 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.216 2.440 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.231 2.440 nonbonded pdb=" OE1 GLU A 21 " pdb=" OG SER S 52 " model vdw 2.243 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.273 2.440 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.288 2.440 ... (remaining 73907 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: 0.680 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: 4.000 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 26.830 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.002 0.032 9322 Z= 0.149 Angle : 0.642 13.876 12619 Z= 0.366 Chirality : 0.043 0.170 1403 Planarity : 0.004 0.051 1597 Dihedral : 14.201 90.715 3354 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.25), residues: 1136 helix: 1.76 (0.27), residues: 396 sheet: -0.03 (0.34), residues: 246 loop : -1.73 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 310 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE S 80 TYR 0.014 0.001 TYR S 103 ARG 0.006 0.000 ARG R 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.934 Fit side-chains REVERT: B 42 ARG cc_start: 0.7311 (ptm-80) cc_final: 0.6910 (tmt170) REVERT: R 262 ILE cc_start: 0.7961 (tt) cc_final: 0.7675 (tt) REVERT: S 20 LEU cc_start: 0.6905 (mt) cc_final: 0.6616 (mt) REVERT: Y 21 MET cc_start: 0.5427 (pmm) cc_final: 0.4650 (mtp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1867 time to fit residues: 40.2809 Evaluate side-chains 127 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 HIS S 35 HIS S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9322 Z= 0.399 Angle : 0.686 8.543 12619 Z= 0.357 Chirality : 0.047 0.155 1403 Planarity : 0.005 0.051 1597 Dihedral : 4.899 56.573 1260 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.92 % Allowed : 8.49 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.25), residues: 1136 helix: 1.29 (0.26), residues: 392 sheet: -0.27 (0.33), residues: 266 loop : -1.85 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 310 HIS 0.006 0.002 HIS B 311 PHE 0.029 0.002 PHE R 165 TYR 0.016 0.002 TYR S 103 ARG 0.006 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6939 (tt0) cc_final: 0.6573 (tm-30) REVERT: B 42 ARG cc_start: 0.7550 (ptm-80) cc_final: 0.7082 (tmt170) REVERT: B 138 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7227 (mm-30) REVERT: B 153 ASP cc_start: 0.8123 (t0) cc_final: 0.7908 (t0) REVERT: B 247 ASP cc_start: 0.8207 (t70) cc_final: 0.7924 (t0) REVERT: R 88 CYS cc_start: 0.7445 (t) cc_final: 0.6426 (m) REVERT: R 91 PHE cc_start: 0.8290 (m-80) cc_final: 0.8008 (m-80) REVERT: R 165 PHE cc_start: 0.8498 (p90) cc_final: 0.8219 (p90) REVERT: S 20 LEU cc_start: 0.6897 (mt) cc_final: 0.6613 (mt) REVERT: S 172 THR cc_start: 0.7900 (m) cc_final: 0.7389 (t) REVERT: S 233 LEU cc_start: 0.4705 (tp) cc_final: 0.4444 (tp) outliers start: 19 outliers final: 15 residues processed: 143 average time/residue: 0.1998 time to fit residues: 40.9367 Evaluate side-chains 146 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 131 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 50 HIS Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 99 SER Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 10.0000 chunk 111 optimal weight: 5.9990 chunk 91 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 82 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** R 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9322 Z= 0.202 Angle : 0.568 10.319 12619 Z= 0.293 Chirality : 0.043 0.212 1403 Planarity : 0.004 0.051 1597 Dihedral : 4.674 55.343 1260 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.72 % Allowed : 12.44 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.25), residues: 1136 helix: 1.42 (0.26), residues: 393 sheet: -0.30 (0.32), residues: 271 loop : -1.79 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 310 HIS 0.009 0.001 HIS R 50 PHE 0.023 0.001 PHE S 80 TYR 0.015 0.001 TYR S 103 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 132 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6951 (tt0) cc_final: 0.6537 (tm-30) REVERT: B 42 ARG cc_start: 0.7584 (ptm-80) cc_final: 0.7138 (tmt170) REVERT: B 153 ASP cc_start: 0.7835 (t0) cc_final: 0.7619 (t0) REVERT: B 247 ASP cc_start: 0.8191 (t70) cc_final: 0.7837 (t0) REVERT: R 88 CYS cc_start: 0.7435 (t) cc_final: 0.6432 (m) REVERT: R 165 PHE cc_start: 0.8437 (p90) cc_final: 0.8135 (p90) REVERT: S 20 LEU cc_start: 0.7008 (mt) cc_final: 0.6705 (mt) REVERT: S 172 THR cc_start: 0.7904 (m) cc_final: 0.7481 (t) outliers start: 17 outliers final: 15 residues processed: 140 average time/residue: 0.1980 time to fit residues: 40.1397 Evaluate side-chains 142 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 9.9990 chunk 77 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 97 optimal weight: 0.0010 chunk 29 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN ** R 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9322 Z= 0.209 Angle : 0.554 7.505 12619 Z= 0.288 Chirality : 0.043 0.235 1403 Planarity : 0.004 0.050 1597 Dihedral : 4.630 56.383 1260 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.43 % Allowed : 13.55 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1136 helix: 1.46 (0.26), residues: 393 sheet: -0.23 (0.32), residues: 271 loop : -1.74 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP R 310 HIS 0.003 0.001 HIS S 167 PHE 0.023 0.001 PHE S 80 TYR 0.016 0.001 TYR A 37 ARG 0.003 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 130 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6941 (tt0) cc_final: 0.6524 (tm-30) REVERT: B 42 ARG cc_start: 0.7698 (ptm-80) cc_final: 0.7202 (tmt170) REVERT: B 153 ASP cc_start: 0.7827 (t0) cc_final: 0.7607 (t0) REVERT: B 247 ASP cc_start: 0.8169 (t70) cc_final: 0.7604 (t0) REVERT: R 88 CYS cc_start: 0.7443 (t) cc_final: 0.6441 (m) REVERT: R 165 PHE cc_start: 0.8405 (p90) cc_final: 0.8096 (p90) REVERT: S 20 LEU cc_start: 0.7060 (mt) cc_final: 0.6759 (mt) REVERT: S 172 THR cc_start: 0.7841 (m) cc_final: 0.7435 (t) REVERT: Y 21 MET cc_start: 0.5701 (pmm) cc_final: 0.4396 (mtm) outliers start: 24 outliers final: 18 residues processed: 144 average time/residue: 0.1962 time to fit residues: 40.3914 Evaluate side-chains 142 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 93 optimal weight: 20.0000 chunk 75 optimal weight: 0.0060 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 98 optimal weight: 0.0040 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.6810 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN R 41 ASN S 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9322 Z= 0.140 Angle : 0.510 8.844 12619 Z= 0.263 Chirality : 0.041 0.141 1403 Planarity : 0.004 0.049 1597 Dihedral : 4.445 54.556 1260 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.12 % Allowed : 15.17 % Favored : 82.71 % 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: -0.15 (0.25), residues: 1136 helix: 1.72 (0.26), residues: 387 sheet: -0.03 (0.33), residues: 264 loop : -1.70 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP R 310 HIS 0.003 0.001 HIS A 357 PHE 0.021 0.001 PHE S 80 TYR 0.014 0.001 TYR A 37 ARG 0.002 0.000 ARG S 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.002 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6918 (tt0) cc_final: 0.6506 (tm-30) REVERT: B 42 ARG cc_start: 0.7675 (ptm-80) cc_final: 0.7236 (tmt170) REVERT: B 247 ASP cc_start: 0.8132 (t70) cc_final: 0.7555 (t0) REVERT: R 161 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7655 (tt) REVERT: R 165 PHE cc_start: 0.8382 (p90) cc_final: 0.8005 (p90) REVERT: S 20 LEU cc_start: 0.7040 (mt) cc_final: 0.6719 (mt) REVERT: S 172 THR cc_start: 0.7766 (m) cc_final: 0.7385 (t) REVERT: Y 21 MET cc_start: 0.5293 (pmm) cc_final: 0.4994 (ppp) outliers start: 21 outliers final: 16 residues processed: 135 average time/residue: 0.1920 time to fit residues: 37.6381 Evaluate side-chains 136 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 119 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.0670 chunk 21 optimal weight: 0.0040 chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 109 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 50 optimal weight: 0.0670 chunk 9 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.8272 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9322 Z= 0.154 Angle : 0.509 7.889 12619 Z= 0.263 Chirality : 0.041 0.194 1403 Planarity : 0.004 0.049 1597 Dihedral : 4.407 55.036 1260 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 2.63 % Allowed : 16.18 % Favored : 81.19 % 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: -0.15 (0.25), residues: 1136 helix: 1.74 (0.26), residues: 388 sheet: -0.10 (0.33), residues: 262 loop : -1.67 (0.26), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 310 HIS 0.003 0.001 HIS A 357 PHE 0.020 0.001 PHE S 80 TYR 0.015 0.001 TYR A 37 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 125 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7681 (ptm-80) cc_final: 0.7246 (tmt170) REVERT: B 247 ASP cc_start: 0.8131 (t70) cc_final: 0.7549 (t0) REVERT: R 161 LEU cc_start: 0.7945 (OUTLIER) cc_final: 0.7608 (tt) REVERT: R 165 PHE cc_start: 0.8406 (p90) cc_final: 0.8065 (p90) REVERT: R 262 ILE cc_start: 0.8751 (tp) cc_final: 0.8316 (tp) REVERT: S 20 LEU cc_start: 0.7055 (mt) cc_final: 0.6732 (mt) REVERT: S 172 THR cc_start: 0.7689 (m) cc_final: 0.7370 (t) REVERT: Y 21 MET cc_start: 0.4913 (OUTLIER) cc_final: 0.4649 (ppp) outliers start: 26 outliers final: 19 residues processed: 138 average time/residue: 0.1880 time to fit residues: 37.7363 Evaluate side-chains 140 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 126 CYS Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 21 MET Chi-restraints excluded: chain Y residue 30 VAL Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 108 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 50 optimal weight: 0.2980 chunk 67 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9322 Z= 0.139 Angle : 0.509 8.683 12619 Z= 0.259 Chirality : 0.041 0.132 1403 Planarity : 0.004 0.048 1597 Dihedral : 4.346 54.347 1260 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.53 % Allowed : 17.19 % Favored : 80.28 % 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: -0.05 (0.25), residues: 1136 helix: 1.78 (0.26), residues: 390 sheet: 0.09 (0.34), residues: 255 loop : -1.66 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP R 310 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.001 PHE A 212 TYR 0.015 0.001 TYR A 37 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 117 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7696 (ptm-80) cc_final: 0.7294 (tmt170) REVERT: B 247 ASP cc_start: 0.8121 (t70) cc_final: 0.7541 (t0) REVERT: R 20 ASN cc_start: 0.3635 (OUTLIER) cc_final: 0.2996 (p0) REVERT: R 161 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7610 (tt) REVERT: R 165 PHE cc_start: 0.8390 (p90) cc_final: 0.8027 (p90) REVERT: R 262 ILE cc_start: 0.8744 (tp) cc_final: 0.8313 (tp) REVERT: R 273 MET cc_start: 0.7100 (mtp) cc_final: 0.6872 (mtp) REVERT: S 20 LEU cc_start: 0.7007 (mt) cc_final: 0.6677 (mt) REVERT: S 172 THR cc_start: 0.7672 (m) cc_final: 0.7383 (t) REVERT: Y 21 MET cc_start: 0.4895 (OUTLIER) cc_final: 0.4691 (ppp) outliers start: 25 outliers final: 20 residues processed: 129 average time/residue: 0.1907 time to fit residues: 35.7445 Evaluate side-chains 140 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 117 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 20 ASN Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 21 MET Chi-restraints excluded: chain Y residue 30 VAL Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9322 Z= 0.217 Angle : 0.551 9.211 12619 Z= 0.283 Chirality : 0.042 0.136 1403 Planarity : 0.004 0.048 1597 Dihedral : 4.488 56.394 1260 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 2.83 % Allowed : 17.39 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1136 helix: 1.70 (0.27), residues: 389 sheet: -0.08 (0.33), residues: 262 loop : -1.66 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 310 HIS 0.003 0.001 HIS R 63 PHE 0.022 0.001 PHE S 80 TYR 0.015 0.001 TYR A 37 ARG 0.009 0.000 ARG R 23 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 128 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7737 (ptm-80) cc_final: 0.7317 (tmt170) REVERT: B 247 ASP cc_start: 0.8141 (t70) cc_final: 0.7562 (t0) REVERT: R 88 CYS cc_start: 0.7458 (t) cc_final: 0.6426 (m) REVERT: R 161 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7609 (tt) REVERT: R 262 ILE cc_start: 0.8749 (tp) cc_final: 0.8322 (tp) REVERT: R 273 MET cc_start: 0.7124 (mtp) cc_final: 0.6910 (mtp) REVERT: S 20 LEU cc_start: 0.7026 (mt) cc_final: 0.6696 (mt) REVERT: S 172 THR cc_start: 0.7600 (m) cc_final: 0.7332 (t) outliers start: 28 outliers final: 25 residues processed: 143 average time/residue: 0.1796 time to fit residues: 37.9159 Evaluate side-chains 150 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 30 VAL Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.8980 chunk 104 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 79 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 107 optimal weight: 9.9990 chunk 65 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 20 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9322 Z= 0.156 Angle : 0.534 10.157 12619 Z= 0.269 Chirality : 0.041 0.134 1403 Planarity : 0.004 0.049 1597 Dihedral : 4.409 55.136 1260 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.43 % Allowed : 18.50 % Favored : 79.07 % 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: -0.12 (0.25), residues: 1136 helix: 1.72 (0.26), residues: 391 sheet: -0.03 (0.33), residues: 260 loop : -1.67 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP R 310 HIS 0.003 0.001 HIS A 357 PHE 0.022 0.001 PHE S 80 TYR 0.015 0.001 TYR A 37 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 124 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7739 (ptm-80) cc_final: 0.7355 (tmt170) REVERT: B 247 ASP cc_start: 0.8118 (t70) cc_final: 0.7535 (t0) REVERT: R 88 CYS cc_start: 0.7449 (t) cc_final: 0.6433 (m) REVERT: R 161 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7592 (tt) REVERT: R 262 ILE cc_start: 0.8738 (tp) cc_final: 0.8316 (tp) REVERT: R 273 MET cc_start: 0.7126 (mtp) cc_final: 0.6905 (mtp) REVERT: S 172 THR cc_start: 0.7526 (m) cc_final: 0.7253 (t) outliers start: 24 outliers final: 20 residues processed: 136 average time/residue: 0.1852 time to fit residues: 36.7947 Evaluate side-chains 145 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 30 VAL Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 0.0060 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9322 Z= 0.188 Angle : 0.545 9.572 12619 Z= 0.276 Chirality : 0.042 0.134 1403 Planarity : 0.004 0.048 1597 Dihedral : 4.471 55.888 1260 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 2.33 % Allowed : 18.40 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.12 (0.25), residues: 1136 helix: 1.74 (0.26), residues: 391 sheet: -0.06 (0.33), residues: 262 loop : -1.66 (0.26), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP R 310 HIS 0.003 0.001 HIS A 357 PHE 0.025 0.001 PHE R 165 TYR 0.015 0.001 TYR A 37 ARG 0.004 0.000 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 42 ARG cc_start: 0.7775 (ptm-80) cc_final: 0.7389 (tmt170) REVERT: B 247 ASP cc_start: 0.8144 (t70) cc_final: 0.7570 (t0) REVERT: R 23 ARG cc_start: 0.8217 (mpt-90) cc_final: 0.7909 (mpt180) REVERT: R 88 CYS cc_start: 0.7450 (t) cc_final: 0.6445 (m) REVERT: R 161 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7630 (tt) REVERT: R 165 PHE cc_start: 0.8381 (p90) cc_final: 0.8075 (p90) REVERT: R 262 ILE cc_start: 0.8753 (tp) cc_final: 0.8424 (tp) REVERT: R 273 MET cc_start: 0.7138 (mtp) cc_final: 0.6922 (mtp) REVERT: S 172 THR cc_start: 0.7518 (m) cc_final: 0.7255 (t) outliers start: 23 outliers final: 22 residues processed: 138 average time/residue: 0.1805 time to fit residues: 36.4800 Evaluate side-chains 149 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 136 ASN Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 30 VAL Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 89 optimal weight: 20.0000 chunk 37 optimal weight: 0.3980 chunk 92 optimal weight: 20.0000 chunk 11 optimal weight: 0.0370 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 64 optimal weight: 0.0670 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.213053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135839 restraints weight = 9589.692| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 2.83 r_work: 0.3463 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9322 Z= 0.132 Angle : 0.525 9.490 12619 Z= 0.265 Chirality : 0.041 0.192 1403 Planarity : 0.004 0.049 1597 Dihedral : 4.377 56.281 1260 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.12 % Allowed : 19.21 % Favored : 78.67 % 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: -0.04 (0.25), residues: 1136 helix: 1.77 (0.26), residues: 388 sheet: 0.12 (0.34), residues: 255 loop : -1.62 (0.25), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP R 310 HIS 0.003 0.001 HIS B 225 PHE 0.023 0.001 PHE S 80 TYR 0.015 0.001 TYR A 37 ARG 0.004 0.000 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2230.89 seconds wall clock time: 41 minutes 23.14 seconds (2483.14 seconds total)