Starting phenix.real_space_refine on Mon Mar 11 12:22:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/03_2024/8w89_37349_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/03_2024/8w89_37349.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/03_2024/8w89_37349.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/03_2024/8w89_37349.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/03_2024/8w89_37349_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w89_37349/03_2024/8w89_37349_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 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 61 5.16 5 C 5229 2.51 5 N 1419 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 61": "NH1" <-> "NH2" Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 169": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8230 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1934 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2283 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 31 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PEA': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.97, per 1000 atoms: 0.60 Number of scatterers: 8230 At special positions: 0 Unit cell: (81.536, 100.672, 132.288, 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 61 16.00 O 1521 8.00 N 1419 7.00 C 5229 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " 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: 3.31 Conformation dependent library (CDL) restraints added in 1.5 seconds 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 10 sheets defined 37.5% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 13 through 34 Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 99 through 101 No H-bonds generated for 'chain 'A' and resid 99 through 101' Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 184 through 203 removed outlier: 3.650A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 20 through 51 Processing helix chain 'R' and resid 57 through 75 removed outlier: 3.607A pdb=" N LEU R 61 " --> pdb=" O PRO R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 84 Processing helix chain 'R' and resid 93 through 126 Processing helix chain 'R' and resid 131 through 134 No H-bonds generated for 'chain 'R' and resid 131 through 134' Processing helix chain 'R' and resid 137 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 179 Processing helix chain 'R' and resid 188 through 198 Processing helix chain 'R' and resid 200 through 230 Processing helix chain 'R' and resid 248 through 274 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 283 through 305 removed outlier: 3.619A pdb=" N TRP R 291 " --> pdb=" O ASP R 287 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 315 Processing sheet with id= A, first strand: chain 'A' and resid 211 through 215 removed outlier: 7.378A pdb=" N VAL A 139 " --> pdb=" O TYR A 212 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N HIS A 214 " --> pdb=" O VAL A 139 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU A 141 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ASN A 80 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LEU A 43 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N HIS A 82 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N LEU A 45 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N PHE A 84 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A 70 " --> pdb=" O ASP A 85 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.732A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.122A 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: 6.886A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.787A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.881A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.163A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.185A 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: 6.507A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.518A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.740A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 6 removed outlier: 3.503A pdb=" N LEU N 18 " --> pdb=" O MET N 83 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.136A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 386 hydrogen bonds defined for protein. 1128 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: 2.72 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1806 1.33 - 1.46: 2217 1.46 - 1.58: 4297 1.58 - 1.71: 0 1.71 - 1.84: 88 Bond restraints: 8408 Sorted by residual: bond pdb=" CA TYR R 122 " pdb=" C TYR R 122 " ideal model delta sigma weight residual 1.524 1.471 0.053 1.27e-02 6.20e+03 1.75e+01 bond pdb=" CA ARG N 98 " pdb=" C ARG N 98 " ideal model delta sigma weight residual 1.526 1.474 0.052 1.37e-02 5.33e+03 1.43e+01 bond pdb=" CA THR A 216 " pdb=" C THR A 216 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.21e-02 6.83e+03 1.18e+01 bond pdb=" CA TRP B 297 " pdb=" C TRP B 297 " ideal model delta sigma weight residual 1.523 1.485 0.039 1.18e-02 7.18e+03 1.07e+01 bond pdb=" CA ASN R 296 " pdb=" C ASN R 296 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.02e+01 ... (remaining 8403 not shown) Histogram of bond angle deviations from ideal: 100.17 - 106.98: 221 106.98 - 113.80: 4620 113.80 - 120.62: 3572 120.62 - 127.44: 2886 127.44 - 134.25: 89 Bond angle restraints: 11388 Sorted by residual: angle pdb=" N GLN R 53 " pdb=" CA GLN R 53 " pdb=" C GLN R 53 " ideal model delta sigma weight residual 113.38 104.99 8.39 1.23e+00 6.61e-01 4.65e+01 angle pdb=" N HIS R 50 " pdb=" CA HIS R 50 " pdb=" C HIS R 50 " ideal model delta sigma weight residual 111.36 118.67 -7.31 1.09e+00 8.42e-01 4.50e+01 angle pdb=" N ARG R 23 " pdb=" CA ARG R 23 " pdb=" C ARG R 23 " ideal model delta sigma weight residual 111.28 104.39 6.89 1.09e+00 8.42e-01 3.99e+01 angle pdb=" N GLN B 259 " pdb=" CA GLN B 259 " pdb=" C GLN B 259 " ideal model delta sigma weight residual 109.14 117.78 -8.64 1.49e+00 4.50e-01 3.36e+01 angle pdb=" N ASP B 228 " pdb=" CA ASP B 228 " pdb=" C ASP B 228 " ideal model delta sigma weight residual 110.24 117.28 -7.04 1.47e+00 4.63e-01 2.29e+01 ... (remaining 11383 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.55: 4545 17.55 - 35.10: 367 35.10 - 52.65: 68 52.65 - 70.20: 12 70.20 - 87.75: 5 Dihedral angle restraints: 4997 sinusoidal: 1957 harmonic: 3040 Sorted by residual: dihedral pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CA ASP B 258 " pdb=" CB ASP B 258 " ideal model delta harmonic sigma weight residual 122.80 132.20 -9.40 0 2.50e+00 1.60e-01 1.41e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 62.27 30.73 1 1.00e+01 1.00e-02 1.35e+01 dihedral pdb=" C VAL R 288 " pdb=" N VAL R 288 " pdb=" CA VAL R 288 " pdb=" CB VAL R 288 " ideal model delta harmonic sigma weight residual -122.00 -130.56 8.56 0 2.50e+00 1.60e-01 1.17e+01 ... (remaining 4994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1083 0.076 - 0.152: 146 0.152 - 0.229: 29 0.229 - 0.305: 11 0.305 - 0.381: 3 Chirality restraints: 1272 Sorted by residual: chirality pdb=" CA ASP B 258 " pdb=" N ASP B 258 " pdb=" C ASP B 258 " pdb=" CB ASP B 258 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CA PHE R 268 " pdb=" N PHE R 268 " pdb=" C PHE R 268 " pdb=" CB PHE R 268 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA TRP A 96 " pdb=" N TRP A 96 " pdb=" C TRP A 96 " pdb=" CB TRP A 96 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 1269 not shown) Planarity restraints: 1452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 94 " 0.016 2.00e-02 2.50e+03 3.13e-02 9.82e+00 pdb=" C VAL R 94 " -0.054 2.00e-02 2.50e+03 pdb=" O VAL R 94 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE R 95 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 48 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.23e+00 pdb=" C ILE R 48 " 0.053 2.00e-02 2.50e+03 pdb=" O ILE R 48 " -0.019 2.00e-02 2.50e+03 pdb=" N SER R 49 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS R 265 " 0.044 5.00e-02 4.00e+02 6.70e-02 7.18e+00 pdb=" N PRO R 266 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO R 266 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 266 " 0.039 5.00e-02 4.00e+02 ... (remaining 1449 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 2858 2.85 - 3.36: 7764 3.36 - 3.87: 13973 3.87 - 4.39: 16331 4.39 - 4.90: 28041 Nonbonded interactions: 68967 Sorted by model distance: nonbonded pdb=" O SER B 67 " pdb=" OG SER B 67 " model vdw 2.334 2.440 nonbonded pdb=" OG1 THR R 37 " pdb=" OG1 THR R 298 " model vdw 2.368 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.382 2.440 nonbonded pdb=" O SER R 115 " pdb=" OG SER R 118 " model vdw 2.407 2.440 nonbonded pdb=" ND1 HIS B 311 " pdb=" OG SER B 331 " model vdw 2.430 2.520 ... (remaining 68962 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: 3.280 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: 6.150 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.610 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 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 : 0.006 0.053 8408 Z= 0.392 Angle : 0.826 10.489 11388 Z= 0.525 Chirality : 0.063 0.381 1272 Planarity : 0.005 0.067 1452 Dihedral : 13.331 87.748 3024 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.90 % Allowed : 2.24 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.26), residues: 1031 helix: 2.05 (0.26), residues: 392 sheet: 0.11 (0.36), residues: 216 loop : -0.58 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 96 HIS 0.002 0.001 HIS R 63 PHE 0.023 0.002 PHE B 235 TYR 0.021 0.001 TYR A 210 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 156 time to evaluate : 0.850 Fit side-chains REVERT: B 34 THR cc_start: 0.8595 (p) cc_final: 0.8055 (p) REVERT: B 175 GLN cc_start: 0.7708 (mm-40) cc_final: 0.7335 (mp10) REVERT: G 21 MET cc_start: 0.7482 (mtm) cc_final: 0.7240 (mmt) REVERT: R 182 CYS cc_start: 0.5280 (OUTLIER) cc_final: 0.4802 (p) outliers start: 8 outliers final: 0 residues processed: 163 average time/residue: 1.1541 time to fit residues: 200.2264 Evaluate side-chains 131 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 10.0000 chunk 51 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 GLN A 223 ASN B 88 ASN B 259 GLN R 53 GLN R 175 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8408 Z= 0.203 Angle : 0.525 6.117 11388 Z= 0.280 Chirality : 0.043 0.355 1272 Planarity : 0.004 0.045 1452 Dihedral : 4.513 58.690 1142 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.57 % Allowed : 12.01 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1031 helix: 2.23 (0.26), residues: 400 sheet: 0.15 (0.35), residues: 199 loop : -0.59 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS R 63 PHE 0.018 0.001 PHE A 70 TYR 0.018 0.001 TYR A 210 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 THR cc_start: 0.8610 (p) cc_final: 0.8213 (p) REVERT: B 175 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7413 (mp10) REVERT: B 293 ASN cc_start: 0.7690 (m-40) cc_final: 0.7380 (p0) REVERT: R 273 MET cc_start: 0.7704 (mmm) cc_final: 0.7416 (mmm) outliers start: 14 outliers final: 6 residues processed: 143 average time/residue: 1.0967 time to fit residues: 167.7381 Evaluate side-chains 132 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 126 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 10 GLU Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 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 101 ASN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 88 ASN B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8408 Z= 0.253 Angle : 0.536 6.967 11388 Z= 0.284 Chirality : 0.043 0.298 1272 Planarity : 0.004 0.038 1452 Dihedral : 4.578 56.488 1142 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.69 % Allowed : 13.58 % Favored : 83.73 % 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: 0.89 (0.26), residues: 1031 helix: 2.13 (0.25), residues: 401 sheet: 0.07 (0.35), residues: 205 loop : -0.62 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS R 63 PHE 0.043 0.002 PHE A 70 TYR 0.022 0.001 TYR A 210 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: B 175 GLN cc_start: 0.7763 (mm-40) cc_final: 0.7359 (mp10) REVERT: B 269 ILE cc_start: 0.8534 (mm) cc_final: 0.8170 (mm) REVERT: B 293 ASN cc_start: 0.7718 (m-40) cc_final: 0.7494 (p0) REVERT: R 166 LYS cc_start: 0.7917 (mmtt) cc_final: 0.7604 (mptp) outliers start: 24 outliers final: 9 residues processed: 150 average time/residue: 1.1427 time to fit residues: 182.6726 Evaluate side-chains 145 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 171 ILE Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 97 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 26 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 144 ASN A 146 GLN B 75 GLN B 88 ASN B 259 GLN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8408 Z= 0.201 Angle : 0.517 6.866 11388 Z= 0.273 Chirality : 0.042 0.320 1272 Planarity : 0.003 0.035 1452 Dihedral : 4.457 53.512 1142 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.69 % Allowed : 15.38 % Favored : 81.93 % 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: 0.88 (0.26), residues: 1031 helix: 2.04 (0.26), residues: 401 sheet: 0.18 (0.37), residues: 186 loop : -0.58 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.003 0.001 HIS A 209 PHE 0.032 0.001 PHE A 70 TYR 0.029 0.001 TYR R 172 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: B 175 GLN cc_start: 0.7836 (mm-40) cc_final: 0.7406 (mp10) REVERT: G 42 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.6720 (mp0) REVERT: R 166 LYS cc_start: 0.7754 (mmtt) cc_final: 0.7472 (mptp) outliers start: 24 outliers final: 6 residues processed: 153 average time/residue: 1.1646 time to fit residues: 189.7692 Evaluate side-chains 142 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 135 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 146 GLN B 88 ASN B 220 GLN B 259 GLN ** B 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8408 Z= 0.194 Angle : 0.515 7.865 11388 Z= 0.273 Chirality : 0.042 0.325 1272 Planarity : 0.003 0.037 1452 Dihedral : 4.381 53.155 1142 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.92 % Allowed : 16.72 % Favored : 80.36 % 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: 0.83 (0.26), residues: 1031 helix: 2.02 (0.25), residues: 401 sheet: 0.10 (0.36), residues: 186 loop : -0.59 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.004 0.001 HIS A 82 PHE 0.044 0.001 PHE A 70 TYR 0.018 0.001 TYR R 172 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 137 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: G 42 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6741 (mp0) REVERT: N 83 MET cc_start: 0.8050 (mtp) cc_final: 0.7823 (mtp) REVERT: R 77 MET cc_start: 0.8322 (mtt) cc_final: 0.7947 (mtt) REVERT: R 105 MET cc_start: 0.8046 (ttt) cc_final: 0.7582 (ttt) REVERT: R 166 LYS cc_start: 0.7730 (mmtt) cc_final: 0.7452 (mptp) outliers start: 26 outliers final: 11 residues processed: 151 average time/residue: 1.0860 time to fit residues: 175.2946 Evaluate side-chains 147 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 52 LYS Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 182 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN A 146 GLN B 88 ASN B 119 ASN B 259 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8408 Z= 0.177 Angle : 0.508 9.224 11388 Z= 0.269 Chirality : 0.042 0.366 1272 Planarity : 0.003 0.039 1452 Dihedral : 4.287 51.051 1142 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.69 % Allowed : 17.73 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1031 helix: 2.05 (0.25), residues: 401 sheet: 0.11 (0.36), residues: 187 loop : -0.55 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.003 0.001 HIS A 209 PHE 0.038 0.001 PHE A 70 TYR 0.013 0.001 TYR N 60 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 137 time to evaluate : 0.942 Fit side-chains revert: symmetry clash REVERT: B 101 MET cc_start: 0.8503 (mtp) cc_final: 0.8199 (mtp) REVERT: B 269 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8172 (mm) REVERT: G 42 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.6804 (mp0) REVERT: N 83 MET cc_start: 0.8000 (mtp) cc_final: 0.7784 (mtp) REVERT: R 77 MET cc_start: 0.8152 (mtt) cc_final: 0.7842 (mtt) outliers start: 24 outliers final: 9 residues processed: 150 average time/residue: 1.1298 time to fit residues: 180.7938 Evaluate side-chains 140 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 129 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 0.2980 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 ASN A 146 GLN B 75 GLN B 259 GLN B 293 ASN ** N 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8408 Z= 0.177 Angle : 0.513 11.136 11388 Z= 0.271 Chirality : 0.042 0.383 1272 Planarity : 0.003 0.041 1452 Dihedral : 4.228 49.325 1142 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.47 % Allowed : 18.41 % Favored : 79.12 % 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: 0.85 (0.26), residues: 1031 helix: 2.01 (0.25), residues: 401 sheet: 0.18 (0.35), residues: 180 loop : -0.58 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 310 HIS 0.003 0.001 HIS A 209 PHE 0.044 0.001 PHE A 70 TYR 0.016 0.001 TYR N 60 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8524 (mtp) cc_final: 0.8227 (mtp) REVERT: B 234 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.8830 (m-80) REVERT: B 269 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8158 (mm) REVERT: N 83 MET cc_start: 0.7978 (mtp) cc_final: 0.7769 (mtp) REVERT: R 77 MET cc_start: 0.8094 (mtt) cc_final: 0.7671 (mtt) REVERT: R 166 LYS cc_start: 0.7082 (mptp) cc_final: 0.6786 (mptp) outliers start: 22 outliers final: 12 residues processed: 144 average time/residue: 1.1005 time to fit residues: 169.1175 Evaluate side-chains 144 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.0370 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 88 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8408 Z= 0.181 Angle : 0.523 12.010 11388 Z= 0.275 Chirality : 0.042 0.391 1272 Planarity : 0.003 0.043 1452 Dihedral : 4.187 47.334 1142 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.58 % Allowed : 19.53 % Favored : 77.89 % 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: 0.82 (0.26), residues: 1031 helix: 1.98 (0.26), residues: 401 sheet: 0.12 (0.35), residues: 182 loop : -0.58 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP R 310 HIS 0.003 0.001 HIS A 209 PHE 0.042 0.001 PHE A 70 TYR 0.019 0.001 TYR N 60 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 140 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 LYS cc_start: 0.7910 (mmmt) cc_final: 0.7683 (mtpt) REVERT: B 101 MET cc_start: 0.8524 (mtp) cc_final: 0.8220 (mtp) REVERT: B 234 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.8812 (m-80) REVERT: N 83 MET cc_start: 0.8001 (mtp) cc_final: 0.7783 (mtp) REVERT: R 158 MET cc_start: 0.7259 (ttm) cc_final: 0.6445 (ttm) REVERT: R 166 LYS cc_start: 0.7060 (mptp) cc_final: 0.6740 (mptp) outliers start: 23 outliers final: 11 residues processed: 154 average time/residue: 1.1621 time to fit residues: 190.7698 Evaluate side-chains 142 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 0.5980 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8408 Z= 0.193 Angle : 0.545 13.207 11388 Z= 0.283 Chirality : 0.043 0.437 1272 Planarity : 0.003 0.043 1452 Dihedral : 4.213 45.946 1142 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.13 % Allowed : 20.09 % Favored : 77.78 % 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: 0.86 (0.26), residues: 1031 helix: 1.93 (0.25), residues: 401 sheet: 0.08 (0.35), residues: 197 loop : -0.45 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 310 HIS 0.003 0.001 HIS A 209 PHE 0.046 0.001 PHE A 70 TYR 0.018 0.001 TYR N 60 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 157 LYS cc_start: 0.7894 (mmmt) cc_final: 0.7639 (mtpt) REVERT: B 101 MET cc_start: 0.8543 (mtp) cc_final: 0.8235 (mtp) REVERT: B 234 PHE cc_start: 0.9286 (OUTLIER) cc_final: 0.8824 (m-80) REVERT: N 83 MET cc_start: 0.8016 (mtp) cc_final: 0.7776 (mtp) REVERT: R 158 MET cc_start: 0.7294 (ttm) cc_final: 0.6537 (ttm) REVERT: R 166 LYS cc_start: 0.7076 (mptp) cc_final: 0.6748 (mptp) outliers start: 19 outliers final: 13 residues processed: 144 average time/residue: 1.1397 time to fit residues: 175.4092 Evaluate side-chains 142 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 128 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 100 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 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 75 GLN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 8408 Z= 0.208 Angle : 0.547 13.180 11388 Z= 0.286 Chirality : 0.043 0.430 1272 Planarity : 0.003 0.044 1452 Dihedral : 4.250 44.820 1142 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.80 % Allowed : 20.54 % Favored : 77.67 % 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: 0.79 (0.26), residues: 1031 helix: 1.92 (0.25), residues: 400 sheet: 0.07 (0.35), residues: 187 loop : -0.54 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 310 HIS 0.003 0.001 HIS A 209 PHE 0.045 0.001 PHE A 70 TYR 0.019 0.001 TYR N 60 ARG 0.003 0.000 ARG N 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2062 Ramachandran restraints generated. 1031 Oldfield, 0 Emsley, 1031 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 136 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 101 MET cc_start: 0.8556 (mtp) cc_final: 0.8241 (mtp) REVERT: B 234 PHE cc_start: 0.9295 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: N 83 MET cc_start: 0.8034 (mtp) cc_final: 0.7780 (mtp) REVERT: R 158 MET cc_start: 0.7343 (ttm) cc_final: 0.6618 (ttm) REVERT: R 166 LYS cc_start: 0.7100 (mptp) cc_final: 0.6768 (mptp) outliers start: 16 outliers final: 13 residues processed: 149 average time/residue: 1.1443 time to fit residues: 181.7713 Evaluate side-chains 146 residues out of total 898 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 132 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain N residue 86 LEU Chi-restraints excluded: chain R residue 96 CYS Chi-restraints excluded: chain R residue 149 SER Chi-restraints excluded: chain R residue 182 CYS Chi-restraints excluded: chain R residue 265 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 0.1980 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.159888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.126254 restraints weight = 10416.230| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.42 r_work: 0.3384 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 8408 Z= 0.189 Angle : 0.551 13.637 11388 Z= 0.285 Chirality : 0.042 0.436 1272 Planarity : 0.003 0.044 1452 Dihedral : 4.200 43.244 1142 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.91 % Allowed : 20.76 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.26), residues: 1031 helix: 1.90 (0.26), residues: 401 sheet: 0.04 (0.35), residues: 187 loop : -0.55 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 310 HIS 0.003 0.001 HIS A 209 PHE 0.044 0.001 PHE A 70 TYR 0.019 0.001 TYR N 60 ARG 0.003 0.000 ARG N 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3365.51 seconds wall clock time: 60 minutes 38.30 seconds (3638.30 seconds total)