Starting phenix.real_space_refine on Tue Feb 13 23:08:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4d_31448/02_2024/7f4d_31448.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4d_31448/02_2024/7f4d_31448.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/7f4d_31448/02_2024/7f4d_31448.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4d_31448/02_2024/7f4d_31448.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4d_31448/02_2024/7f4d_31448.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f4d_31448/02_2024/7f4d_31448.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= 0.003 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 Ca 1 9.91 5 S 56 5.16 5 C 5102 2.51 5 N 1411 2.21 5 O 1477 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8047 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 234, 1942 Classifications: {'peptide': 234} Link IDs: {'PTRANS': 6, 'TRANS': 227} Chain breaks: 1 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: "B" Number of atoms: 2575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2575 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "R" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 263, 2028 Classifications: {'peptide': 263} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 256} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 101 Classifications: {'peptide': 12} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 10} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.59, per 1000 atoms: 0.57 Number of scatterers: 8047 At special positions: 0 Unit cell: (120.175, 99.275, 84.645, 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) Ca 1 19.99 S 56 16.00 O 1477 8.00 N 1411 7.00 C 5102 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 267 " - pdb=" SG CYS R 273 " distance=2.04 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1942 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 10 sheets defined 45.0% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.596A pdb=" N ALA G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 59 through 63 removed outlier: 3.721A pdb=" N ARG G 62 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU G 63 " --> pdb=" O PRO G 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 59 through 63' Processing helix chain 'A' and resid 13 through 39 Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 252 through 279 removed outlier: 3.980A pdb=" N GLN A 267 " --> pdb=" O TYR A 253 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N GLU A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 4.177A pdb=" N THR A 284 " --> pdb=" O TRP A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 307 through 311 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 331 through 353 removed outlier: 3.677A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'R' and resid 43 through 66 removed outlier: 4.143A pdb=" N SER R 47 " --> pdb=" O GLY R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 70 Processing helix chain 'R' and resid 71 through 103 Processing helix chain 'R' and resid 109 through 148 Processing helix chain 'R' and resid 151 through 156 Processing helix chain 'R' and resid 157 through 182 Processing helix chain 'R' and resid 185 through 226 removed outlier: 3.785A pdb=" N LEU R 189 " --> pdb=" O HIS R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 238 through 267 removed outlier: 3.517A pdb=" N PHE R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) Proline residue: R 256 - end of helix Processing helix chain 'R' and resid 270 through 278 Processing helix chain 'R' and resid 279 through 299 Proline residue: R 295 - end of helix Processing helix chain 'R' and resid 302 through 307 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214 removed outlier: 6.220A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL A 224 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N LEU A 45 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.612A pdb=" N GLN N 5 " --> pdb=" O ALA N 23 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 10 through 12 removed outlier: 5.995A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.542A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.505A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.617A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.600A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.567A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 231 through 234 removed outlier: 6.371A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.348A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1299 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: 2.32 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2239 1.33 - 1.46: 2028 1.46 - 1.59: 3859 1.59 - 1.72: 0 1.72 - 1.85: 77 Bond restraints: 8203 Sorted by residual: bond pdb=" C GLY R 136 " pdb=" O GLY R 136 " ideal model delta sigma weight residual 1.234 1.206 0.028 1.20e-02 6.94e+03 5.39e+00 bond pdb=" C TRP N 47 " pdb=" N VAL N 48 " ideal model delta sigma weight residual 1.333 1.364 -0.030 1.46e-02 4.69e+03 4.31e+00 bond pdb=" CG HIS R 217 " pdb=" CD2 HIS R 217 " ideal model delta sigma weight residual 1.354 1.332 0.022 1.10e-02 8.26e+03 3.92e+00 bond pdb=" C GLU M 5 " pdb=" N HIS M 6 " ideal model delta sigma weight residual 1.335 1.361 -0.026 1.35e-02 5.49e+03 3.71e+00 bond pdb=" CZ ARG A 232 " pdb=" NH2 ARG A 232 " ideal model delta sigma weight residual 1.330 1.305 0.025 1.30e-02 5.92e+03 3.58e+00 ... (remaining 8198 not shown) Histogram of bond angle deviations from ideal: 97.67 - 104.92: 111 104.92 - 112.16: 3856 112.16 - 119.40: 3005 119.40 - 126.65: 4039 126.65 - 133.89: 102 Bond angle restraints: 11113 Sorted by residual: angle pdb=" C ASP B 291 " pdb=" N PHE B 292 " pdb=" CA PHE B 292 " ideal model delta sigma weight residual 121.70 131.26 -9.56 1.80e+00 3.09e-01 2.82e+01 angle pdb=" N ASP B 291 " pdb=" CA ASP B 291 " pdb=" C ASP B 291 " ideal model delta sigma weight residual 112.23 117.02 -4.79 1.26e+00 6.30e-01 1.44e+01 angle pdb=" N PHE M 7 " pdb=" CA PHE M 7 " pdb=" C PHE M 7 " ideal model delta sigma weight residual 108.14 102.64 5.50 1.52e+00 4.33e-01 1.31e+01 angle pdb=" C LEU R 93 " pdb=" N GLU R 94 " pdb=" CA GLU R 94 " ideal model delta sigma weight residual 121.58 114.78 6.80 1.95e+00 2.63e-01 1.22e+01 angle pdb=" C TYR R 148 " pdb=" N ALA R 149 " pdb=" CA ALA R 149 " ideal model delta sigma weight residual 120.38 124.87 -4.49 1.37e+00 5.33e-01 1.07e+01 ... (remaining 11108 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4552 17.62 - 35.24: 280 35.24 - 52.85: 43 52.85 - 70.47: 18 70.47 - 88.09: 2 Dihedral angle restraints: 4895 sinusoidal: 1898 harmonic: 2997 Sorted by residual: dihedral pdb=" CA ASP B 66 " pdb=" C ASP B 66 " pdb=" N SER B 67 " pdb=" CA SER B 67 " ideal model delta harmonic sigma weight residual 180.00 -150.34 -29.66 0 5.00e+00 4.00e-02 3.52e+01 dihedral pdb=" CA CYS B 204 " pdb=" C CYS B 204 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta harmonic sigma weight residual 180.00 151.23 28.77 0 5.00e+00 4.00e-02 3.31e+01 dihedral pdb=" CA TYR B 105 " pdb=" C TYR B 105 " pdb=" N ALA B 106 " pdb=" CA ALA B 106 " ideal model delta harmonic sigma weight residual 180.00 151.53 28.47 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 4892 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 734 0.048 - 0.095: 400 0.095 - 0.143: 119 0.143 - 0.191: 16 0.191 - 0.238: 6 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA VAL B 315 " pdb=" N VAL B 315 " pdb=" C VAL B 315 " pdb=" CB VAL B 315 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CG LEU B 308 " pdb=" CB LEU B 308 " pdb=" CD1 LEU B 308 " pdb=" CD2 LEU B 308 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CA GLU R 94 " pdb=" N GLU R 94 " pdb=" C GLU R 94 " pdb=" CB GLU R 94 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 1272 not shown) Planarity restraints: 1413 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 74 " -0.001 2.00e-02 2.50e+03 2.95e-02 1.74e+01 pdb=" CG TYR R 74 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR R 74 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR R 74 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR R 74 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR R 74 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR R 74 " 0.048 2.00e-02 2.50e+03 pdb=" OH TYR R 74 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 314 " -0.252 9.50e-02 1.11e+02 1.16e-01 1.74e+01 pdb=" NE ARG B 314 " 0.033 2.00e-02 2.50e+03 pdb=" CZ ARG B 314 " -0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG B 314 " 0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG B 314 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " -0.030 2.00e-02 2.50e+03 2.19e-02 1.20e+01 pdb=" CG TRP A 281 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.015 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.011 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.002 2.00e-02 2.50e+03 ... (remaining 1410 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 70 2.59 - 3.17: 7184 3.17 - 3.74: 13253 3.74 - 4.32: 19002 4.32 - 4.90: 31194 Nonbonded interactions: 70703 Sorted by model distance: nonbonded pdb=" OD1 ASP R 117 " pdb="CA CA R 501 " model vdw 2.011 2.510 nonbonded pdb=" O GLU M 5 " pdb="CA CA R 501 " model vdw 2.068 2.510 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.235 2.440 nonbonded pdb=" O SER R 127 " pdb=" OG SER R 131 " model vdw 2.256 2.440 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.289 2.440 ... (remaining 70698 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.110 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.790 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 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:12.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.009 0.068 8203 Z= 0.610 Angle : 1.066 9.555 11113 Z= 0.630 Chirality : 0.060 0.238 1275 Planarity : 0.010 0.121 1413 Dihedral : 12.497 88.088 2947 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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 (0.24), residues: 1014 helix: -0.12 (0.22), residues: 402 sheet: -0.18 (0.37), residues: 211 loop : -1.16 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.009 TRP A 281 HIS 0.016 0.004 HIS R 153 PHE 0.030 0.005 PHE A 246 TYR 0.048 0.007 TYR R 74 ARG 0.053 0.005 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 248 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 16 VAL cc_start: 0.8961 (t) cc_final: 0.8760 (p) REVERT: G 20 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8257 (mtmm) REVERT: G 21 MET cc_start: 0.8619 (mpp) cc_final: 0.8245 (mpm) REVERT: G 22 GLU cc_start: 0.8542 (tt0) cc_final: 0.8139 (tm-30) REVERT: G 29 LYS cc_start: 0.9165 (mmtt) cc_final: 0.8742 (mmmt) REVERT: G 32 LYS cc_start: 0.9141 (tttt) cc_final: 0.8804 (ttmm) REVERT: A 29 GLN cc_start: 0.8388 (tp40) cc_final: 0.7833 (mm-40) REVERT: A 221 MET cc_start: 0.8799 (ttm) cc_final: 0.8418 (ttm) REVERT: A 271 ASN cc_start: 0.8766 (m-40) cc_final: 0.8526 (m110) REVERT: A 378 ASP cc_start: 0.8018 (m-30) cc_final: 0.7533 (m-30) REVERT: N 18 LEU cc_start: 0.8998 (tp) cc_final: 0.8782 (tp) REVERT: N 38 ARG cc_start: 0.8576 (ptt180) cc_final: 0.8190 (ptt-90) REVERT: N 46 GLU cc_start: 0.7696 (tt0) cc_final: 0.7233 (tt0) REVERT: N 76 LYS cc_start: 0.9087 (mtpp) cc_final: 0.8624 (mtpm) REVERT: N 80 TYR cc_start: 0.8438 (m-80) cc_final: 0.8036 (m-80) REVERT: N 90 ASP cc_start: 0.8585 (m-30) cc_final: 0.7887 (m-30) REVERT: N 107 CYS cc_start: 0.8354 (m) cc_final: 0.5531 (m) REVERT: N 123 GLN cc_start: 0.8480 (tp40) cc_final: 0.8108 (mm-40) REVERT: B 9 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8740 (tm-30) REVERT: B 169 TRP cc_start: 0.8921 (m100) cc_final: 0.8409 (m100) REVERT: B 186 ASP cc_start: 0.7074 (t0) cc_final: 0.6774 (t0) REVERT: B 209 LYS cc_start: 0.8501 (mttm) cc_final: 0.8283 (mttm) REVERT: B 262 MET cc_start: 0.7954 (tpp) cc_final: 0.7549 (tpp) REVERT: B 277 SER cc_start: 0.9016 (t) cc_final: 0.8740 (t) REVERT: B 337 LYS cc_start: 0.7765 (mttt) cc_final: 0.7484 (mmmm) REVERT: R 56 ASN cc_start: 0.9245 (m-40) cc_final: 0.8937 (m110) REVERT: R 91 ASN cc_start: 0.8500 (t0) cc_final: 0.8114 (t0) REVERT: R 303 GLN cc_start: 0.8351 (mm110) cc_final: 0.7490 (mm-40) REVERT: M 7 PHE cc_start: 0.8802 (t80) cc_final: 0.8542 (t80) outliers start: 0 outliers final: 0 residues processed: 248 average time/residue: 1.2482 time to fit residues: 326.2384 Evaluate side-chains 168 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 58 optimal weight: 0.0970 chunk 90 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 75 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8203 Z= 0.203 Angle : 0.646 8.149 11113 Z= 0.338 Chirality : 0.041 0.136 1275 Planarity : 0.004 0.039 1413 Dihedral : 5.271 23.402 1120 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.07 % Allowed : 12.56 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.63 (0.26), residues: 1014 helix: 1.71 (0.24), residues: 403 sheet: -0.24 (0.36), residues: 208 loop : -0.47 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 339 HIS 0.004 0.001 HIS R 260 PHE 0.016 0.002 PHE G 61 TYR 0.016 0.002 TYR N 95 ARG 0.006 0.001 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 183 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8481 (mtm110) cc_final: 0.8268 (mtm110) REVERT: G 14 LYS cc_start: 0.9434 (mmpt) cc_final: 0.9214 (mmpt) REVERT: G 22 GLU cc_start: 0.8652 (tt0) cc_final: 0.8369 (tm-30) REVERT: G 36 ASP cc_start: 0.8375 (m-30) cc_final: 0.8166 (m-30) REVERT: A 16 ASP cc_start: 0.8873 (t0) cc_final: 0.8620 (t0) REVERT: A 50 ASN cc_start: 0.8903 (p0) cc_final: 0.8375 (p0) REVERT: A 268 GLU cc_start: 0.8558 (tt0) cc_final: 0.8302 (tt0) REVERT: A 378 ASP cc_start: 0.8137 (m-30) cc_final: 0.7714 (m-30) REVERT: N 38 ARG cc_start: 0.8958 (ptt180) cc_final: 0.8303 (ptt180) REVERT: N 46 GLU cc_start: 0.7977 (tt0) cc_final: 0.7344 (tt0) REVERT: N 73 ASP cc_start: 0.8221 (t0) cc_final: 0.8007 (t0) REVERT: N 82 GLN cc_start: 0.9129 (tp40) cc_final: 0.8890 (tp40) REVERT: N 87 LYS cc_start: 0.8799 (OUTLIER) cc_final: 0.8243 (ptpt) REVERT: N 90 ASP cc_start: 0.8690 (m-30) cc_final: 0.7934 (m-30) REVERT: N 120 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8522 (mm110) REVERT: B 172 GLU cc_start: 0.8003 (pp20) cc_final: 0.7733 (pp20) REVERT: B 186 ASP cc_start: 0.6838 (t0) cc_final: 0.6410 (t0) REVERT: B 188 MET cc_start: 0.7971 (mmm) cc_final: 0.7484 (mmm) REVERT: B 262 MET cc_start: 0.7881 (tpp) cc_final: 0.7233 (ttm) REVERT: B 267 ASP cc_start: 0.8719 (p0) cc_final: 0.8358 (p0) REVERT: B 275 SER cc_start: 0.8577 (t) cc_final: 0.8314 (m) REVERT: B 277 SER cc_start: 0.9067 (t) cc_final: 0.8800 (t) REVERT: R 56 ASN cc_start: 0.9209 (m-40) cc_final: 0.8990 (m110) REVERT: R 126 SER cc_start: 0.8751 (t) cc_final: 0.8520 (m) REVERT: R 303 GLN cc_start: 0.8157 (mm110) cc_final: 0.7609 (mm-40) REVERT: M 11 LYS cc_start: 0.9281 (mppt) cc_final: 0.8980 (mmmm) outliers start: 18 outliers final: 4 residues processed: 193 average time/residue: 1.1451 time to fit residues: 234.6260 Evaluate side-chains 156 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 151 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain N residue 87 LYS Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 25 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 0.0470 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 72 optimal weight: 8.9990 chunk 89 optimal weight: 0.8980 overall best weight: 2.1882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8203 Z= 0.306 Angle : 0.631 7.959 11113 Z= 0.325 Chirality : 0.042 0.160 1275 Planarity : 0.004 0.033 1413 Dihedral : 4.874 22.833 1120 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.88 % Allowed : 15.09 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 1014 helix: 2.14 (0.24), residues: 407 sheet: -0.51 (0.35), residues: 204 loop : -0.50 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 169 HIS 0.006 0.001 HIS M 6 PHE 0.018 0.002 PHE G 61 TYR 0.018 0.002 TYR N 95 ARG 0.005 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 14 LYS cc_start: 0.9406 (mmpt) cc_final: 0.9159 (mmpt) REVERT: G 21 MET cc_start: 0.8660 (mmp) cc_final: 0.8122 (mmp) REVERT: G 22 GLU cc_start: 0.8585 (tt0) cc_final: 0.8353 (tm-30) REVERT: G 28 ILE cc_start: 0.9364 (pt) cc_final: 0.9140 (pp) REVERT: G 29 LYS cc_start: 0.9279 (mmmt) cc_final: 0.8972 (mptp) REVERT: G 36 ASP cc_start: 0.8416 (m-30) cc_final: 0.8166 (m-30) REVERT: A 16 ASP cc_start: 0.8902 (t0) cc_final: 0.8651 (t0) REVERT: A 50 ASN cc_start: 0.8977 (p0) cc_final: 0.8736 (p0) REVERT: A 268 GLU cc_start: 0.8622 (tt0) cc_final: 0.8374 (tt0) REVERT: A 378 ASP cc_start: 0.8131 (m-30) cc_final: 0.7838 (m-30) REVERT: N 38 ARG cc_start: 0.9118 (ptt180) cc_final: 0.8459 (ptm160) REVERT: N 46 GLU cc_start: 0.8115 (tt0) cc_final: 0.7447 (tt0) REVERT: N 80 TYR cc_start: 0.8085 (m-80) cc_final: 0.7580 (m-80) REVERT: N 82 GLN cc_start: 0.9165 (tp40) cc_final: 0.8915 (tp40) REVERT: N 90 ASP cc_start: 0.8929 (m-30) cc_final: 0.8404 (m-30) REVERT: B 30 LEU cc_start: 0.8965 (tp) cc_final: 0.8420 (tp) REVERT: B 105 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8486 (m-80) REVERT: B 172 GLU cc_start: 0.8180 (pp20) cc_final: 0.7886 (pp20) REVERT: B 186 ASP cc_start: 0.6838 (t0) cc_final: 0.6294 (t0) REVERT: B 188 MET cc_start: 0.7984 (mmm) cc_final: 0.7480 (mmm) REVERT: B 217 MET cc_start: 0.8422 (pmm) cc_final: 0.8066 (pmt) REVERT: B 262 MET cc_start: 0.7897 (tpp) cc_final: 0.7470 (ttm) REVERT: B 275 SER cc_start: 0.8738 (OUTLIER) cc_final: 0.8379 (m) REVERT: B 277 SER cc_start: 0.9320 (t) cc_final: 0.9106 (t) REVERT: R 126 SER cc_start: 0.8837 (t) cc_final: 0.8587 (m) REVERT: R 303 GLN cc_start: 0.8163 (mm110) cc_final: 0.7626 (mm-40) REVERT: M 11 LYS cc_start: 0.9311 (mppt) cc_final: 0.9006 (mmmm) outliers start: 25 outliers final: 11 residues processed: 176 average time/residue: 1.2368 time to fit residues: 231.8445 Evaluate side-chains 162 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 149 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 244 THR Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 301 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.9980 chunk 43 optimal weight: 0.0030 chunk 61 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN A 267 GLN A 271 ASN A 387 HIS N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8203 Z= 0.208 Angle : 0.611 9.502 11113 Z= 0.310 Chirality : 0.041 0.148 1275 Planarity : 0.004 0.054 1413 Dihedral : 4.607 21.697 1120 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.76 % Allowed : 16.13 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % 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: 0.98 (0.27), residues: 1014 helix: 2.36 (0.24), residues: 407 sheet: -0.56 (0.34), residues: 209 loop : -0.41 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.002 PHE G 61 TYR 0.017 0.001 TYR N 95 ARG 0.013 0.000 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8690 (ttm110) cc_final: 0.8365 (mtm110) REVERT: G 17 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8296 (tp30) REVERT: G 21 MET cc_start: 0.8569 (mmp) cc_final: 0.8062 (mmp) REVERT: G 22 GLU cc_start: 0.8595 (tt0) cc_final: 0.8347 (tm-30) REVERT: G 32 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8591 (tppp) REVERT: G 36 ASP cc_start: 0.8426 (m-30) cc_final: 0.8114 (m-30) REVERT: A 50 ASN cc_start: 0.8960 (p0) cc_final: 0.8714 (p0) REVERT: A 271 ASN cc_start: 0.8822 (m110) cc_final: 0.8547 (m110) REVERT: A 378 ASP cc_start: 0.8131 (m-30) cc_final: 0.7832 (m-30) REVERT: N 3 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7189 (tm130) REVERT: N 38 ARG cc_start: 0.9109 (ptt180) cc_final: 0.8660 (ptt180) REVERT: N 46 GLU cc_start: 0.8107 (tt0) cc_final: 0.7579 (tt0) REVERT: N 80 TYR cc_start: 0.7995 (m-80) cc_final: 0.7587 (m-80) REVERT: N 82 GLN cc_start: 0.9173 (tp40) cc_final: 0.8730 (tp40) REVERT: N 87 LYS cc_start: 0.8785 (ptpp) cc_final: 0.8517 (ptpp) REVERT: N 90 ASP cc_start: 0.8859 (m-30) cc_final: 0.8533 (m-30) REVERT: B 30 LEU cc_start: 0.8776 (tp) cc_final: 0.8374 (tp) REVERT: B 105 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8488 (m-80) REVERT: B 172 GLU cc_start: 0.8204 (pp20) cc_final: 0.7960 (pp20) REVERT: B 186 ASP cc_start: 0.6804 (t0) cc_final: 0.6262 (t0) REVERT: B 188 MET cc_start: 0.7854 (mmm) cc_final: 0.7343 (mmm) REVERT: B 217 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8080 (pmt) REVERT: B 262 MET cc_start: 0.7838 (tpp) cc_final: 0.7578 (ttm) REVERT: B 275 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8415 (m) REVERT: R 126 SER cc_start: 0.8792 (t) cc_final: 0.8538 (m) REVERT: R 303 GLN cc_start: 0.8158 (mm110) cc_final: 0.7653 (mm-40) REVERT: M 5 GLU cc_start: 0.8942 (mm-30) cc_final: 0.8379 (tt0) REVERT: M 11 LYS cc_start: 0.9385 (mppt) cc_final: 0.8979 (mppt) outliers start: 24 outliers final: 7 residues processed: 169 average time/residue: 1.1289 time to fit residues: 203.2098 Evaluate side-chains 157 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 146 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain R residue 188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 39 optimal weight: 0.0020 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 132 ASN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8203 Z= 0.201 Angle : 0.588 7.638 11113 Z= 0.298 Chirality : 0.040 0.151 1275 Planarity : 0.003 0.034 1413 Dihedral : 4.438 20.769 1120 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.11 % Allowed : 17.63 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1014 helix: 2.52 (0.24), residues: 407 sheet: -0.56 (0.34), residues: 210 loop : -0.37 (0.32), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS B 54 PHE 0.013 0.001 PHE G 61 TYR 0.019 0.002 TYR G 40 ARG 0.008 0.000 ARG R 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 164 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8696 (ttm110) cc_final: 0.8344 (mtm110) REVERT: G 14 LYS cc_start: 0.9372 (mppt) cc_final: 0.9060 (mmpt) REVERT: G 17 GLU cc_start: 0.8822 (tm-30) cc_final: 0.8367 (tp30) REVERT: G 21 MET cc_start: 0.8594 (mmp) cc_final: 0.8059 (mmp) REVERT: G 22 GLU cc_start: 0.8585 (tt0) cc_final: 0.8338 (tm-30) REVERT: G 32 LYS cc_start: 0.8918 (ttmm) cc_final: 0.8671 (tppp) REVERT: G 36 ASP cc_start: 0.8445 (m-30) cc_final: 0.8063 (m-30) REVERT: A 50 ASN cc_start: 0.8941 (p0) cc_final: 0.8582 (p0) REVERT: A 271 ASN cc_start: 0.8861 (m110) cc_final: 0.8578 (m110) REVERT: A 378 ASP cc_start: 0.8152 (m-30) cc_final: 0.7853 (m-30) REVERT: N 3 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.7350 (tm130) REVERT: N 33 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8203 (tmtp) REVERT: N 38 ARG cc_start: 0.9130 (ptt180) cc_final: 0.8783 (ptt180) REVERT: N 46 GLU cc_start: 0.8156 (tt0) cc_final: 0.7705 (tt0) REVERT: N 73 ASP cc_start: 0.7889 (t0) cc_final: 0.7270 (t0) REVERT: N 80 TYR cc_start: 0.7689 (m-80) cc_final: 0.7417 (m-80) REVERT: N 82 GLN cc_start: 0.9085 (tp40) cc_final: 0.8754 (tp40) REVERT: N 87 LYS cc_start: 0.8822 (ptpp) cc_final: 0.8517 (ptpp) REVERT: N 90 ASP cc_start: 0.8872 (m-30) cc_final: 0.8561 (m-30) REVERT: B 31 SER cc_start: 0.9256 (t) cc_final: 0.9045 (p) REVERT: B 105 TYR cc_start: 0.8962 (OUTLIER) cc_final: 0.8427 (m-80) REVERT: B 172 GLU cc_start: 0.8259 (pp20) cc_final: 0.8009 (pp20) REVERT: B 188 MET cc_start: 0.7825 (mmm) cc_final: 0.7487 (mmm) REVERT: B 209 LYS cc_start: 0.8579 (mttm) cc_final: 0.8251 (mttm) REVERT: B 217 MET cc_start: 0.8473 (OUTLIER) cc_final: 0.8153 (pmt) REVERT: B 262 MET cc_start: 0.7828 (tpp) cc_final: 0.7351 (ttm) REVERT: B 275 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8410 (m) REVERT: B 325 MET cc_start: 0.8612 (tpp) cc_final: 0.8277 (mmm) REVERT: R 126 SER cc_start: 0.8848 (t) cc_final: 0.8586 (m) REVERT: R 303 GLN cc_start: 0.7810 (mm110) cc_final: 0.7403 (mm-40) REVERT: M 5 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8690 (tt0) REVERT: M 11 LYS cc_start: 0.9397 (mppt) cc_final: 0.9007 (mmmm) outliers start: 27 outliers final: 11 residues processed: 179 average time/residue: 1.0852 time to fit residues: 207.0578 Evaluate side-chains 167 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 151 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 301 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 23 optimal weight: 0.0980 chunk 96 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN B 36 ASN ** R 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8203 Z= 0.234 Angle : 0.603 8.056 11113 Z= 0.303 Chirality : 0.040 0.148 1275 Planarity : 0.003 0.031 1413 Dihedral : 4.364 20.154 1120 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.00 % Allowed : 19.70 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.27), residues: 1014 helix: 2.64 (0.24), residues: 407 sheet: -0.63 (0.34), residues: 214 loop : -0.27 (0.33), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 339 HIS 0.003 0.001 HIS A 357 PHE 0.013 0.002 PHE G 61 TYR 0.022 0.002 TYR G 40 ARG 0.006 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 0.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8731 (ttm110) cc_final: 0.8343 (mtm110) REVERT: G 14 LYS cc_start: 0.9389 (mppt) cc_final: 0.8986 (mmtm) REVERT: G 17 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8344 (tp30) REVERT: G 21 MET cc_start: 0.8630 (mmp) cc_final: 0.8073 (mmp) REVERT: G 22 GLU cc_start: 0.8611 (tt0) cc_final: 0.8314 (tm-30) REVERT: G 32 LYS cc_start: 0.8924 (ttmm) cc_final: 0.8679 (tppp) REVERT: G 36 ASP cc_start: 0.8390 (m-30) cc_final: 0.7990 (m-30) REVERT: A 50 ASN cc_start: 0.8978 (p0) cc_final: 0.8602 (p0) REVERT: A 271 ASN cc_start: 0.8863 (m110) cc_final: 0.8588 (m110) REVERT: A 378 ASP cc_start: 0.8134 (m-30) cc_final: 0.7840 (m-30) REVERT: N 33 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.8138 (tmtp) REVERT: N 46 GLU cc_start: 0.8233 (tt0) cc_final: 0.7764 (tt0) REVERT: N 53 GLN cc_start: 0.8618 (mp10) cc_final: 0.8288 (mm-40) REVERT: N 76 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8550 (mtmm) REVERT: N 80 TYR cc_start: 0.7756 (m-80) cc_final: 0.7449 (m-80) REVERT: N 82 GLN cc_start: 0.9110 (tp40) cc_final: 0.8667 (tp40) REVERT: N 87 LYS cc_start: 0.8715 (ptpp) cc_final: 0.8416 (ptpp) REVERT: N 90 ASP cc_start: 0.8843 (m-30) cc_final: 0.8584 (m-30) REVERT: B 9 GLN cc_start: 0.9061 (mm-40) cc_final: 0.8827 (mm-40) REVERT: B 31 SER cc_start: 0.9235 (t) cc_final: 0.9028 (p) REVERT: B 105 TYR cc_start: 0.8980 (OUTLIER) cc_final: 0.8354 (m-80) REVERT: B 172 GLU cc_start: 0.8285 (pp20) cc_final: 0.8006 (pp20) REVERT: B 188 MET cc_start: 0.7838 (mmm) cc_final: 0.7498 (mmm) REVERT: B 209 LYS cc_start: 0.8571 (mttm) cc_final: 0.8272 (mttm) REVERT: B 217 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8247 (pmt) REVERT: B 275 SER cc_start: 0.8755 (OUTLIER) cc_final: 0.8364 (m) REVERT: B 325 MET cc_start: 0.8615 (tpp) cc_final: 0.8278 (mmm) REVERT: R 91 ASN cc_start: 0.8456 (t0) cc_final: 0.8244 (t0) REVERT: R 126 SER cc_start: 0.8848 (t) cc_final: 0.8592 (m) REVERT: R 303 GLN cc_start: 0.7789 (mm110) cc_final: 0.7392 (mm-40) REVERT: M 11 LYS cc_start: 0.9430 (mppt) cc_final: 0.9040 (mmmm) outliers start: 26 outliers final: 13 residues processed: 170 average time/residue: 1.0807 time to fit residues: 195.8442 Evaluate side-chains 169 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 188 VAL Chi-restraints excluded: chain R residue 301 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 96 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 0.0370 chunk 57 optimal weight: 3.9990 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN B 32 GLN B 36 ASN B 156 GLN R 219 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8203 Z= 0.188 Angle : 0.602 9.614 11113 Z= 0.300 Chirality : 0.040 0.140 1275 Planarity : 0.003 0.038 1413 Dihedral : 4.306 19.653 1120 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.00 % Allowed : 20.05 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 1014 helix: 2.67 (0.24), residues: 408 sheet: -0.57 (0.34), residues: 208 loop : -0.32 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE A 376 TYR 0.023 0.002 TYR G 40 ARG 0.007 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 9 ILE cc_start: 0.8962 (tp) cc_final: 0.8705 (tp) REVERT: G 13 ARG cc_start: 0.8725 (ttm110) cc_final: 0.8149 (mtm110) REVERT: G 14 LYS cc_start: 0.9411 (mppt) cc_final: 0.9113 (mmtm) REVERT: G 17 GLU cc_start: 0.8847 (tm-30) cc_final: 0.8400 (tp30) REVERT: G 21 MET cc_start: 0.8623 (mmp) cc_final: 0.8064 (mmp) REVERT: G 22 GLU cc_start: 0.8628 (tt0) cc_final: 0.8308 (tm-30) REVERT: G 36 ASP cc_start: 0.8355 (m-30) cc_final: 0.8063 (m-30) REVERT: G 38 MET cc_start: 0.8706 (ttp) cc_final: 0.8427 (ttp) REVERT: A 271 ASN cc_start: 0.8840 (m110) cc_final: 0.8571 (m110) REVERT: A 378 ASP cc_start: 0.8136 (m-30) cc_final: 0.7835 (m-30) REVERT: N 3 GLN cc_start: 0.7725 (OUTLIER) cc_final: 0.7349 (tm130) REVERT: N 33 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.7876 (tmtp) REVERT: N 46 GLU cc_start: 0.8221 (tt0) cc_final: 0.7826 (tt0) REVERT: N 53 GLN cc_start: 0.8563 (mp10) cc_final: 0.8252 (mm-40) REVERT: N 82 GLN cc_start: 0.9046 (tp40) cc_final: 0.8665 (tp40) REVERT: N 87 LYS cc_start: 0.8857 (ptpp) cc_final: 0.8528 (ptpp) REVERT: N 90 ASP cc_start: 0.8902 (m-30) cc_final: 0.8659 (m-30) REVERT: B 9 GLN cc_start: 0.9094 (mm-40) cc_final: 0.8823 (mm-40) REVERT: B 105 TYR cc_start: 0.8908 (OUTLIER) cc_final: 0.8304 (m-80) REVERT: B 172 GLU cc_start: 0.8281 (pp20) cc_final: 0.8021 (pp20) REVERT: B 188 MET cc_start: 0.7779 (mmm) cc_final: 0.7432 (mmm) REVERT: B 209 LYS cc_start: 0.8489 (mttm) cc_final: 0.8219 (mttm) REVERT: B 275 SER cc_start: 0.8723 (OUTLIER) cc_final: 0.8331 (m) REVERT: B 325 MET cc_start: 0.8603 (tpp) cc_final: 0.8283 (mmm) REVERT: R 73 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7888 (ppp) REVERT: R 91 ASN cc_start: 0.8506 (t0) cc_final: 0.8273 (t0) REVERT: R 126 SER cc_start: 0.8851 (t) cc_final: 0.8593 (m) REVERT: R 183 TYR cc_start: 0.9130 (p90) cc_final: 0.8786 (p90) REVERT: R 290 ASN cc_start: 0.8171 (t0) cc_final: 0.7728 (t0) REVERT: R 303 GLN cc_start: 0.7606 (mm110) cc_final: 0.7300 (mm-40) REVERT: M 5 GLU cc_start: 0.8378 (tt0) cc_final: 0.7778 (tt0) REVERT: M 11 LYS cc_start: 0.9424 (mppt) cc_final: 0.9085 (mmmm) outliers start: 26 outliers final: 11 residues processed: 176 average time/residue: 1.0841 time to fit residues: 203.6635 Evaluate side-chains 163 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 73 MET Chi-restraints excluded: chain R residue 301 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.0270 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 92 optimal weight: 10.0000 chunk 84 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 overall best weight: 1.3442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN A 31 GLN N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN B 36 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8203 Z= 0.240 Angle : 0.638 9.861 11113 Z= 0.315 Chirality : 0.041 0.136 1275 Planarity : 0.003 0.033 1413 Dihedral : 4.314 19.105 1120 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.57 % Allowed : 20.05 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1014 helix: 2.65 (0.25), residues: 409 sheet: -0.54 (0.34), residues: 218 loop : -0.28 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.002 PHE G 61 TYR 0.022 0.002 TYR G 40 ARG 0.007 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 157 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8715 (ttm110) cc_final: 0.8140 (mtm110) REVERT: G 14 LYS cc_start: 0.9423 (mppt) cc_final: 0.9097 (mmtm) REVERT: G 19 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8953 (mm) REVERT: A 271 ASN cc_start: 0.8834 (m110) cc_final: 0.8559 (m110) REVERT: A 378 ASP cc_start: 0.8141 (m-30) cc_final: 0.7844 (m-30) REVERT: N 3 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7320 (tm130) REVERT: N 6 GLU cc_start: 0.7452 (mt-10) cc_final: 0.7104 (mt-10) REVERT: N 33 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8101 (tmtp) REVERT: N 46 GLU cc_start: 0.8217 (tt0) cc_final: 0.7815 (tt0) REVERT: N 82 GLN cc_start: 0.9047 (tp40) cc_final: 0.8593 (tp40) REVERT: N 87 LYS cc_start: 0.8734 (ptpp) cc_final: 0.8462 (ptpp) REVERT: N 90 ASP cc_start: 0.8741 (m-30) cc_final: 0.8524 (m-30) REVERT: B 9 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8882 (mm-40) REVERT: B 105 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8331 (m-80) REVERT: B 172 GLU cc_start: 0.8302 (pp20) cc_final: 0.8032 (pp20) REVERT: B 188 MET cc_start: 0.7858 (mmm) cc_final: 0.7465 (mmm) REVERT: B 209 LYS cc_start: 0.8509 (mttm) cc_final: 0.8247 (mttm) REVERT: B 217 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8378 (pmm) REVERT: B 275 SER cc_start: 0.8749 (OUTLIER) cc_final: 0.8351 (m) REVERT: B 325 MET cc_start: 0.8545 (tpp) cc_final: 0.8210 (mmm) REVERT: R 91 ASN cc_start: 0.8526 (t0) cc_final: 0.8297 (t0) REVERT: R 126 SER cc_start: 0.8857 (t) cc_final: 0.8593 (m) REVERT: R 183 TYR cc_start: 0.9121 (p90) cc_final: 0.8837 (p90) REVERT: R 238 LYS cc_start: 0.8597 (tttm) cc_final: 0.8312 (tmmt) REVERT: R 303 GLN cc_start: 0.7618 (mm110) cc_final: 0.7315 (mm-40) REVERT: M 5 GLU cc_start: 0.8239 (tt0) cc_final: 0.7670 (tt0) REVERT: M 11 LYS cc_start: 0.9431 (mppt) cc_final: 0.9085 (mmmm) outliers start: 31 outliers final: 16 residues processed: 170 average time/residue: 1.1247 time to fit residues: 203.3077 Evaluate side-chains 169 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 147 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 301 HIS Chi-restraints excluded: chain R residue 305 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 chunk 39 optimal weight: 0.0050 chunk 70 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 94 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.4595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8203 Z= 0.209 Angle : 0.677 10.489 11113 Z= 0.334 Chirality : 0.040 0.156 1275 Planarity : 0.003 0.036 1413 Dihedral : 4.261 17.728 1120 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 3.11 % Allowed : 21.66 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.27), residues: 1014 helix: 2.58 (0.25), residues: 409 sheet: -0.47 (0.34), residues: 216 loop : -0.29 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.001 PHE N 29 TYR 0.022 0.001 TYR G 40 ARG 0.008 0.000 ARG N 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 148 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 13 ARG cc_start: 0.8612 (ttm110) cc_final: 0.8378 (mtm110) REVERT: G 18 GLN cc_start: 0.9089 (tp40) cc_final: 0.8870 (tp-100) REVERT: G 32 LYS cc_start: 0.9046 (ttmm) cc_final: 0.8834 (tppp) REVERT: A 271 ASN cc_start: 0.8818 (m110) cc_final: 0.8558 (m110) REVERT: A 378 ASP cc_start: 0.8140 (m-30) cc_final: 0.7837 (m-30) REVERT: N 3 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7310 (tm130) REVERT: N 33 LYS cc_start: 0.8539 (OUTLIER) cc_final: 0.8122 (tmtp) REVERT: N 46 GLU cc_start: 0.8231 (tt0) cc_final: 0.7840 (tt0) REVERT: N 82 GLN cc_start: 0.8986 (tp40) cc_final: 0.8562 (tp40) REVERT: N 87 LYS cc_start: 0.8828 (ptpp) cc_final: 0.8510 (ptpp) REVERT: N 90 ASP cc_start: 0.8773 (m-30) cc_final: 0.8542 (m-30) REVERT: B 10 GLU cc_start: 0.8831 (mp0) cc_final: 0.8528 (pm20) REVERT: B 105 TYR cc_start: 0.8922 (OUTLIER) cc_final: 0.8390 (m-80) REVERT: B 172 GLU cc_start: 0.8303 (pp20) cc_final: 0.8022 (pp20) REVERT: B 188 MET cc_start: 0.7766 (mmm) cc_final: 0.7413 (mmm) REVERT: B 209 LYS cc_start: 0.8491 (mttm) cc_final: 0.8240 (mttm) REVERT: B 217 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8365 (pmm) REVERT: B 267 ASP cc_start: 0.8631 (OUTLIER) cc_final: 0.8407 (p0) REVERT: B 275 SER cc_start: 0.8766 (OUTLIER) cc_final: 0.8383 (m) REVERT: B 325 MET cc_start: 0.8523 (tpp) cc_final: 0.8195 (mmm) REVERT: R 91 ASN cc_start: 0.8521 (t0) cc_final: 0.8296 (t0) REVERT: R 126 SER cc_start: 0.8863 (t) cc_final: 0.8592 (m) REVERT: R 183 TYR cc_start: 0.9120 (p90) cc_final: 0.8834 (p90) REVERT: R 238 LYS cc_start: 0.8567 (tttm) cc_final: 0.8259 (tmmt) REVERT: M 5 GLU cc_start: 0.8208 (tt0) cc_final: 0.7673 (tt0) REVERT: M 11 LYS cc_start: 0.9408 (mppt) cc_final: 0.9072 (mmmm) outliers start: 27 outliers final: 13 residues processed: 162 average time/residue: 1.0956 time to fit residues: 189.4849 Evaluate side-chains 162 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 24 ASN Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 301 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 0.5980 chunk 24 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN B 36 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8203 Z= 0.238 Angle : 0.679 9.875 11113 Z= 0.337 Chirality : 0.041 0.141 1275 Planarity : 0.004 0.037 1413 Dihedral : 4.283 18.096 1120 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.42 % Allowed : 22.24 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.27), residues: 1014 helix: 2.55 (0.24), residues: 409 sheet: -0.54 (0.34), residues: 216 loop : -0.24 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.003 0.001 HIS A 357 PHE 0.014 0.001 PHE N 29 TYR 0.021 0.002 TYR G 40 ARG 0.009 0.000 ARG N 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 0.852 Fit side-chains REVERT: G 13 ARG cc_start: 0.8661 (ttm110) cc_final: 0.8378 (mtm110) REVERT: G 14 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8988 (mmtm) REVERT: G 20 LYS cc_start: 0.8832 (mtmt) cc_final: 0.8315 (mtmm) REVERT: G 32 LYS cc_start: 0.8956 (ttmm) cc_final: 0.8612 (tppp) REVERT: G 36 ASP cc_start: 0.8291 (m-30) cc_final: 0.7991 (m-30) REVERT: A 271 ASN cc_start: 0.8821 (m110) cc_final: 0.8564 (m110) REVERT: A 378 ASP cc_start: 0.8138 (m-30) cc_final: 0.7856 (m-30) REVERT: N 3 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.7434 (tm130) REVERT: N 31 ASN cc_start: 0.9071 (m-40) cc_final: 0.8866 (m110) REVERT: N 33 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8067 (tmtp) REVERT: N 46 GLU cc_start: 0.8275 (tt0) cc_final: 0.7930 (tt0) REVERT: N 82 GLN cc_start: 0.8957 (tp40) cc_final: 0.8486 (tp40) REVERT: N 87 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8394 (ptpp) REVERT: N 90 ASP cc_start: 0.8839 (m-30) cc_final: 0.8624 (m-30) REVERT: B 105 TYR cc_start: 0.8965 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: B 172 GLU cc_start: 0.8323 (pp20) cc_final: 0.8068 (pp20) REVERT: B 188 MET cc_start: 0.7848 (mmm) cc_final: 0.7588 (mmm) REVERT: B 209 LYS cc_start: 0.8512 (mttm) cc_final: 0.8249 (mttm) REVERT: B 217 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8420 (pmm) REVERT: B 275 SER cc_start: 0.8813 (OUTLIER) cc_final: 0.8419 (m) REVERT: B 325 MET cc_start: 0.8556 (tpp) cc_final: 0.8244 (mmm) REVERT: R 91 ASN cc_start: 0.8521 (t0) cc_final: 0.8291 (t0) REVERT: R 126 SER cc_start: 0.8875 (t) cc_final: 0.8604 (m) REVERT: R 238 LYS cc_start: 0.8593 (tttm) cc_final: 0.8280 (tmmt) REVERT: M 5 GLU cc_start: 0.8208 (tt0) cc_final: 0.7720 (tt0) REVERT: M 11 LYS cc_start: 0.9409 (mppt) cc_final: 0.9073 (mmmm) outliers start: 21 outliers final: 12 residues processed: 155 average time/residue: 1.1471 time to fit residues: 189.3381 Evaluate side-chains 160 residues out of total 877 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 14 LYS Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain A residue 264 ASN Chi-restraints excluded: chain N residue 3 GLN Chi-restraints excluded: chain N residue 33 LYS Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 339 TRP Chi-restraints excluded: chain R residue 301 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 0.0980 chunk 4 optimal weight: 0.0370 chunk 57 optimal weight: 2.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 18 GLN N 3 GLN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.089127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.068755 restraints weight = 18207.104| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.12 r_work: 0.2946 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8203 Z= 0.194 Angle : 0.689 11.830 11113 Z= 0.340 Chirality : 0.040 0.184 1275 Planarity : 0.004 0.035 1413 Dihedral : 4.195 17.545 1120 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.65 % Allowed : 22.24 % Favored : 75.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.10 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.27), residues: 1014 helix: 2.51 (0.24), residues: 409 sheet: -0.50 (0.34), residues: 216 loop : -0.28 (0.32), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.014 0.001 PHE N 29 TYR 0.022 0.001 TYR G 40 ARG 0.007 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3745.35 seconds wall clock time: 67 minutes 5.75 seconds (4025.75 seconds total)