Starting phenix.real_space_refine on Mon Mar 11 13:28:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/03_2024/7xp5_33365.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/03_2024/7xp5_33365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/03_2024/7xp5_33365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/03_2024/7xp5_33365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/03_2024/7xp5_33365.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/03_2024/7xp5_33365.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 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 48 5.16 5 C 5347 2.51 5 N 1448 2.21 5 O 1538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ASP 290": "OD1" <-> "OD2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8381 Number of models: 1 Model: "" Number of chains: 5 Chain: "R" Number of atoms: 2424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2424 Classifications: {'peptide': 299} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 290} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'TYR:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1960 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain breaks: 1 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: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 4.77, per 1000 atoms: 0.57 Number of scatterers: 8381 At special positions: 0 Unit cell: (82.16, 102.96, 132.08, 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 48 16.00 O 1538 8.00 N 1448 7.00 C 5347 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 3.22 Conformation dependent library (CDL) restraints added in 1.6 seconds 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1998 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 10 sheets defined 46.1% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'R' and resid 3 through 39 removed outlier: 3.697A pdb=" N ILE R 7 " --> pdb=" O THR R 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 71 Processing helix chain 'R' and resid 77 through 111 Processing helix chain 'R' and resid 115 through 124 Processing helix chain 'R' and resid 124 through 155 Proline residue: R 136 - end of helix Processing helix chain 'R' and resid 155 through 161 removed outlier: 3.520A pdb=" N GLU R 159 " --> pdb=" O THR R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 174 removed outlier: 4.191A pdb=" N TYR R 173 " --> pdb=" O ARG R 169 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 213 removed outlier: 4.372A pdb=" N VAL R 186 " --> pdb=" O LEU R 182 " (cutoff:3.500A) Proline residue: R 187 - end of helix removed outlier: 3.773A pdb=" N HIS R 212 " --> pdb=" O LYS R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 255 removed outlier: 4.790A pdb=" N PHE R 252 " --> pdb=" O SER R 248 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N GLU R 253 " --> pdb=" O VAL R 249 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER R 254 " --> pdb=" O TRP R 250 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 283 Proline residue: R 272 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 301 Processing helix chain 'A' and resid 6 through 35 Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 98 through 104 removed outlier: 3.934A pdb=" N ASN A 104 " --> pdb=" O GLN A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.076A pdb=" N TYR A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 172 removed outlier: 3.618A pdb=" N ALA A 171 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 205 removed outlier: 4.184A pdb=" N THR A 190 " --> pdb=" O ASP A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 247 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 removed outlier: 3.704A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 4.193A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'N' and resid 62 through 65 removed outlier: 3.513A pdb=" N LYS N 65 " --> pdb=" O GLY N 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 79 removed outlier: 4.753A pdb=" N VAL A 89 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N GLY A 43 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL A 142 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N HIS A 217 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 144 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.691A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.697A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.192A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.818A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.543A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.458A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.951A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.554A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 484 hydrogen bonds defined for protein. 1407 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: 2.34 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2716 1.34 - 1.46: 2030 1.46 - 1.58: 3744 1.58 - 1.70: 0 1.70 - 1.81: 68 Bond restraints: 8558 Sorted by residual: bond pdb=" CG LEU A 144 " pdb=" CD2 LEU A 144 " ideal model delta sigma weight residual 1.521 1.485 0.036 3.30e-02 9.18e+02 1.18e+00 bond pdb=" CB GLN B 75 " pdb=" CG GLN B 75 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.09e+00 bond pdb=" CA ARG B 52 " pdb=" CB ARG B 52 " ideal model delta sigma weight residual 1.526 1.541 -0.015 1.70e-02 3.46e+03 8.08e-01 bond pdb=" C GLY N 8 " pdb=" N GLY N 9 " ideal model delta sigma weight residual 1.331 1.318 0.012 1.46e-02 4.69e+03 7.14e-01 bond pdb=" C LYS A 24 " pdb=" O LYS A 24 " ideal model delta sigma weight residual 1.236 1.246 -0.010 1.15e-02 7.56e+03 7.05e-01 ... (remaining 8553 not shown) Histogram of bond angle deviations from ideal: 99.51 - 106.41: 166 106.41 - 113.31: 4707 113.31 - 120.21: 3044 120.21 - 127.11: 3580 127.11 - 134.01: 97 Bond angle restraints: 11594 Sorted by residual: angle pdb=" C ILE B 58 " pdb=" N TYR B 59 " pdb=" CA TYR B 59 " ideal model delta sigma weight residual 122.42 116.39 6.03 1.55e+00 4.16e-01 1.51e+01 angle pdb=" CA ARG A 16 " pdb=" CB ARG A 16 " pdb=" CG ARG A 16 " ideal model delta sigma weight residual 114.10 121.79 -7.69 2.00e+00 2.50e-01 1.48e+01 angle pdb=" CB ARG A 16 " pdb=" CG ARG A 16 " pdb=" CD ARG A 16 " ideal model delta sigma weight residual 111.30 118.01 -6.71 2.30e+00 1.89e-01 8.52e+00 angle pdb=" CA GLU G 17 " pdb=" CB GLU G 17 " pdb=" CG GLU G 17 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.50e+00 angle pdb=" C ASP A 223 " pdb=" CA ASP A 223 " pdb=" CB ASP A 223 " ideal model delta sigma weight residual 110.42 115.85 -5.43 1.99e+00 2.53e-01 7.45e+00 ... (remaining 11589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4678 17.95 - 35.90: 336 35.90 - 53.85: 58 53.85 - 71.80: 3 71.80 - 89.75: 4 Dihedral angle restraints: 5079 sinusoidal: 1998 harmonic: 3081 Sorted by residual: dihedral pdb=" CA GLY B 185 " pdb=" C GLY B 185 " pdb=" N ASP B 186 " pdb=" CA ASP B 186 " ideal model delta harmonic sigma weight residual 180.00 158.85 21.15 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA LYS G 20 " pdb=" C LYS G 20 " pdb=" N MET G 21 " pdb=" CA MET G 21 " ideal model delta harmonic sigma weight residual 180.00 160.09 19.91 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA VAL A 222 " pdb=" C VAL A 222 " pdb=" N ASP A 223 " pdb=" CA ASP A 223 " ideal model delta harmonic sigma weight residual 180.00 161.05 18.95 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 5076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 959 0.045 - 0.090: 280 0.090 - 0.135: 72 0.135 - 0.180: 4 0.180 - 0.225: 2 Chirality restraints: 1317 Sorted by residual: chirality pdb=" CA TYR B 59 " pdb=" N TYR B 59 " pdb=" C TYR B 59 " pdb=" CB TYR B 59 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB THR B 181 " pdb=" CA THR B 181 " pdb=" OG1 THR B 181 " pdb=" CG2 THR B 181 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.32e-01 ... (remaining 1314 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " 0.027 2.00e-02 2.50e+03 2.13e-02 9.09e+00 pdb=" CG TYR B 59 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " 0.009 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.036 5.00e-02 4.00e+02 5.40e-02 4.67e+00 pdb=" N PRO G 49 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 135 " -0.031 5.00e-02 4.00e+02 4.67e-02 3.48e+00 pdb=" N PRO R 136 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO R 136 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 136 " -0.026 5.00e-02 4.00e+02 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 710 2.74 - 3.28: 8541 3.28 - 3.82: 14077 3.82 - 4.36: 16094 4.36 - 4.90: 28353 Nonbonded interactions: 67775 Sorted by model distance: nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.198 2.440 nonbonded pdb=" OG1 THR B 86 " pdb=" OD1 ASN B 88 " model vdw 2.229 2.440 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.237 2.440 nonbonded pdb=" ND2 ASN N 35 " pdb=" OD2 ASP N 109 " model vdw 2.273 2.520 nonbonded pdb=" N THR B 184 " pdb=" OD2 ASP B 205 " model vdw 2.277 2.520 ... (remaining 67770 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 3.910 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.600 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 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 : 0.004 0.036 8558 Z= 0.249 Angle : 0.593 7.687 11594 Z= 0.322 Chirality : 0.043 0.225 1317 Planarity : 0.004 0.054 1466 Dihedral : 12.659 89.748 3081 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 1.69 (0.26), residues: 1047 helix: 2.69 (0.23), residues: 441 sheet: 0.79 (0.34), residues: 221 loop : -0.58 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 339 HIS 0.004 0.001 HIS R 205 PHE 0.019 0.001 PHE A 195 TYR 0.052 0.002 TYR B 59 ARG 0.012 0.001 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: R 22 PHE cc_start: 0.7175 (t80) cc_final: 0.6957 (t80) REVERT: R 162 MET cc_start: 0.4347 (ptt) cc_final: 0.4093 (ptt) REVERT: R 207 LYS cc_start: 0.7918 (ttpt) cc_final: 0.7635 (ttpt) REVERT: R 285 LYS cc_start: 0.8232 (tmtt) cc_final: 0.7940 (tmtt) REVERT: A 123 GLU cc_start: 0.7019 (tt0) cc_final: 0.6742 (tt0) REVERT: A 236 ASP cc_start: 0.7567 (t70) cc_final: 0.7218 (t0) REVERT: B 49 ARG cc_start: 0.6929 (mpt90) cc_final: 0.6616 (mpt90) REVERT: B 76 ASP cc_start: 0.7267 (p0) cc_final: 0.6933 (p0) REVERT: B 314 ARG cc_start: 0.7758 (ptm160) cc_final: 0.7446 (ttt180) REVERT: G 38 MET cc_start: 0.5923 (ppp) cc_final: 0.5517 (ppp) REVERT: N 80 TYR cc_start: 0.7505 (m-80) cc_final: 0.7248 (m-80) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2634 time to fit residues: 94.5227 Evaluate side-chains 265 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 0.9990 chunk 77 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 0.4980 chunk 79 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.0928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8558 Z= 0.215 Angle : 0.527 6.241 11594 Z= 0.285 Chirality : 0.041 0.144 1317 Planarity : 0.004 0.052 1466 Dihedral : 4.428 19.494 1139 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.20 % Allowed : 12.45 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.26), residues: 1047 helix: 2.86 (0.23), residues: 439 sheet: 0.91 (0.35), residues: 219 loop : -0.66 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 97 HIS 0.004 0.001 HIS A 212 PHE 0.022 0.001 PHE A 77 TYR 0.031 0.002 TYR B 59 ARG 0.006 0.000 ARG A 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 273 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: R 22 PHE cc_start: 0.7119 (t80) cc_final: 0.6891 (t80) REVERT: R 162 MET cc_start: 0.4270 (ptt) cc_final: 0.3994 (ptt) REVERT: R 191 THR cc_start: 0.8070 (t) cc_final: 0.7844 (p) REVERT: R 207 LYS cc_start: 0.7902 (ttpt) cc_final: 0.7645 (ttpt) REVERT: R 285 LYS cc_start: 0.8267 (tmtt) cc_final: 0.7911 (tmtt) REVERT: A 59 LEU cc_start: 0.8259 (mp) cc_final: 0.7944 (mp) REVERT: A 123 GLU cc_start: 0.7034 (tt0) cc_final: 0.6764 (tt0) REVERT: A 128 PHE cc_start: 0.8501 (t80) cc_final: 0.8245 (t80) REVERT: A 197 ARG cc_start: 0.8608 (ttp80) cc_final: 0.8341 (ttp-170) REVERT: A 202 ARG cc_start: 0.6915 (mtm180) cc_final: 0.6592 (mtm180) REVERT: A 236 ASP cc_start: 0.7579 (t70) cc_final: 0.7249 (t0) REVERT: B 49 ARG cc_start: 0.7016 (mpt90) cc_final: 0.6801 (mpt90) REVERT: G 38 MET cc_start: 0.5958 (ppp) cc_final: 0.5533 (ppp) REVERT: N 80 TYR cc_start: 0.7487 (m-80) cc_final: 0.7210 (m-80) outliers start: 11 outliers final: 9 residues processed: 275 average time/residue: 0.2712 time to fit residues: 95.3505 Evaluate side-chains 266 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 257 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain N residue 59 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.0000 chunk 77 optimal weight: 0.5980 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.1980 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 143 HIS R 176 ASN ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8558 Z= 0.177 Angle : 0.497 7.707 11594 Z= 0.266 Chirality : 0.040 0.140 1317 Planarity : 0.004 0.047 1466 Dihedral : 4.287 20.079 1139 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.07 % Allowed : 14.30 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.26), residues: 1047 helix: 3.00 (0.23), residues: 439 sheet: 0.96 (0.35), residues: 219 loop : -0.66 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 97 HIS 0.004 0.001 HIS A 212 PHE 0.017 0.001 PHE A 77 TYR 0.022 0.001 TYR B 59 ARG 0.006 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 267 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: R 22 PHE cc_start: 0.7104 (t80) cc_final: 0.6878 (t80) REVERT: R 162 MET cc_start: 0.4319 (ptt) cc_final: 0.4033 (ptt) REVERT: R 191 THR cc_start: 0.8054 (t) cc_final: 0.7830 (p) REVERT: R 207 LYS cc_start: 0.7911 (ttpt) cc_final: 0.7638 (ttpt) REVERT: R 285 LYS cc_start: 0.8242 (tmtt) cc_final: 0.7876 (tmtt) REVERT: A 121 LEU cc_start: 0.7723 (tp) cc_final: 0.7447 (mt) REVERT: A 123 GLU cc_start: 0.7012 (tt0) cc_final: 0.6756 (tt0) REVERT: A 128 PHE cc_start: 0.8495 (t80) cc_final: 0.8261 (t80) REVERT: A 188 ARG cc_start: 0.7578 (mtm-85) cc_final: 0.7306 (mtm-85) REVERT: A 195 PHE cc_start: 0.8066 (t80) cc_final: 0.7658 (t80) REVERT: A 202 ARG cc_start: 0.7059 (mtm180) cc_final: 0.6641 (mtm180) REVERT: A 236 ASP cc_start: 0.7588 (t70) cc_final: 0.7253 (t0) REVERT: B 49 ARG cc_start: 0.7056 (mpt90) cc_final: 0.6796 (mpt90) REVERT: B 314 ARG cc_start: 0.7650 (ptm160) cc_final: 0.7335 (ttt180) REVERT: G 38 MET cc_start: 0.5956 (ppp) cc_final: 0.5520 (ppp) REVERT: N 80 TYR cc_start: 0.7446 (m-80) cc_final: 0.7243 (m-80) outliers start: 19 outliers final: 17 residues processed: 271 average time/residue: 0.2669 time to fit residues: 91.8164 Evaluate side-chains 275 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 258 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 143 HIS Chi-restraints excluded: chain R residue 221 MET Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 79 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 143 HIS R 148 ASN R 176 ASN ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 37 HIS ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8558 Z= 0.315 Angle : 0.541 7.152 11594 Z= 0.290 Chirality : 0.042 0.153 1317 Planarity : 0.004 0.050 1466 Dihedral : 4.431 20.163 1139 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.73 % Allowed : 16.48 % Favored : 80.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.26), residues: 1047 helix: 2.83 (0.23), residues: 438 sheet: 0.86 (0.34), residues: 220 loop : -0.67 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 99 HIS 0.012 0.001 HIS R 143 PHE 0.020 0.002 PHE A 77 TYR 0.019 0.002 TYR B 59 ARG 0.007 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 273 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: R 22 PHE cc_start: 0.7125 (t80) cc_final: 0.6899 (t80) REVERT: R 162 MET cc_start: 0.4502 (ptt) cc_final: 0.4192 (ptt) REVERT: R 207 LYS cc_start: 0.7940 (ttpt) cc_final: 0.7670 (ttpt) REVERT: R 285 LYS cc_start: 0.8336 (tmtt) cc_final: 0.7959 (tmtt) REVERT: A 123 GLU cc_start: 0.7010 (tt0) cc_final: 0.6737 (tt0) REVERT: A 195 PHE cc_start: 0.8178 (t80) cc_final: 0.7818 (t80) REVERT: A 202 ARG cc_start: 0.7030 (mtm180) cc_final: 0.6610 (mtm180) REVERT: A 236 ASP cc_start: 0.7613 (t70) cc_final: 0.7268 (t0) REVERT: B 49 ARG cc_start: 0.7133 (mpt90) cc_final: 0.6798 (mtt90) REVERT: B 153 ASP cc_start: 0.7624 (m-30) cc_final: 0.7390 (m-30) REVERT: B 258 ASP cc_start: 0.7873 (t70) cc_final: 0.7525 (t70) REVERT: B 314 ARG cc_start: 0.7742 (ptm160) cc_final: 0.7436 (ttt180) REVERT: G 25 ILE cc_start: 0.7984 (OUTLIER) cc_final: 0.7714 (mp) REVERT: G 38 MET cc_start: 0.6018 (ppp) cc_final: 0.5585 (ppp) REVERT: N 80 TYR cc_start: 0.7552 (m-80) cc_final: 0.7312 (m-80) outliers start: 25 outliers final: 18 residues processed: 281 average time/residue: 0.2656 time to fit residues: 95.0798 Evaluate side-chains 279 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 260 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 40 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 143 HIS ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN B 239 ASN N 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8558 Z= 0.233 Angle : 0.523 7.885 11594 Z= 0.279 Chirality : 0.041 0.163 1317 Planarity : 0.004 0.050 1466 Dihedral : 4.374 19.994 1139 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.28 % Allowed : 17.69 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.26), residues: 1047 helix: 2.77 (0.23), residues: 445 sheet: 0.84 (0.34), residues: 219 loop : -0.72 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.004 0.001 HIS A 212 PHE 0.023 0.001 PHE A 77 TYR 0.011 0.001 TYR B 59 ARG 0.009 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 267 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: R 22 PHE cc_start: 0.7105 (t80) cc_final: 0.6872 (t80) REVERT: R 162 MET cc_start: 0.4492 (ptt) cc_final: 0.4181 (ptt) REVERT: R 204 LYS cc_start: 0.8399 (ttmm) cc_final: 0.8188 (ttmm) REVERT: R 207 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7660 (ttpt) REVERT: R 285 LYS cc_start: 0.8296 (tmtt) cc_final: 0.7914 (tmtt) REVERT: A 76 LYS cc_start: 0.7959 (mtpp) cc_final: 0.7599 (mtpp) REVERT: A 123 GLU cc_start: 0.7023 (tt0) cc_final: 0.6762 (tt0) REVERT: A 195 PHE cc_start: 0.8128 (t80) cc_final: 0.7750 (t80) REVERT: A 202 ARG cc_start: 0.6994 (mtm180) cc_final: 0.6517 (mtm180) REVERT: A 236 ASP cc_start: 0.7578 (t70) cc_final: 0.7256 (t0) REVERT: B 49 ARG cc_start: 0.7136 (mpt90) cc_final: 0.6760 (mtt90) REVERT: B 153 ASP cc_start: 0.7622 (m-30) cc_final: 0.7384 (m-30) REVERT: B 258 ASP cc_start: 0.7848 (t70) cc_final: 0.7469 (t70) REVERT: B 314 ARG cc_start: 0.7710 (ptm160) cc_final: 0.7434 (ttt180) REVERT: G 25 ILE cc_start: 0.7962 (OUTLIER) cc_final: 0.7711 (mp) REVERT: G 38 MET cc_start: 0.6031 (ppp) cc_final: 0.5600 (ppp) REVERT: N 80 TYR cc_start: 0.7491 (m-80) cc_final: 0.7205 (m-80) outliers start: 30 outliers final: 22 residues processed: 277 average time/residue: 0.2794 time to fit residues: 99.2356 Evaluate side-chains 280 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 257 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 189 THR Chi-restraints excluded: chain R residue 221 MET Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 95 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN B 239 ASN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8558 Z= 0.233 Angle : 0.525 7.866 11594 Z= 0.280 Chirality : 0.041 0.160 1317 Planarity : 0.004 0.047 1466 Dihedral : 4.366 19.625 1139 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.38 % Allowed : 18.23 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.26), residues: 1047 helix: 2.85 (0.23), residues: 439 sheet: 0.82 (0.34), residues: 221 loop : -0.72 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 99 HIS 0.004 0.001 HIS A 212 PHE 0.021 0.001 PHE A 77 TYR 0.011 0.001 TYR B 289 ARG 0.009 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 267 time to evaluate : 1.060 Fit side-chains revert: symmetry clash REVERT: R 22 PHE cc_start: 0.7103 (t80) cc_final: 0.6874 (t80) REVERT: R 109 LYS cc_start: 0.7557 (mmmm) cc_final: 0.7327 (mtpp) REVERT: R 162 MET cc_start: 0.4492 (ptt) cc_final: 0.4169 (ptt) REVERT: R 204 LYS cc_start: 0.8407 (ttmm) cc_final: 0.8185 (ttmm) REVERT: R 207 LYS cc_start: 0.7920 (ttpt) cc_final: 0.7659 (ttpt) REVERT: R 285 LYS cc_start: 0.8292 (tmtt) cc_final: 0.7909 (tmtt) REVERT: A 76 LYS cc_start: 0.7923 (mtpp) cc_final: 0.7569 (mtpp) REVERT: A 121 LEU cc_start: 0.7739 (tp) cc_final: 0.7445 (mt) REVERT: A 123 GLU cc_start: 0.7020 (tt0) cc_final: 0.6778 (tt0) REVERT: A 128 PHE cc_start: 0.8482 (t80) cc_final: 0.8267 (t80) REVERT: A 195 PHE cc_start: 0.8143 (t80) cc_final: 0.7728 (t80) REVERT: A 197 ARG cc_start: 0.8516 (ttp80) cc_final: 0.8226 (ttp-170) REVERT: A 202 ARG cc_start: 0.6979 (mtm180) cc_final: 0.6507 (mtm180) REVERT: A 236 ASP cc_start: 0.7592 (t70) cc_final: 0.7255 (t0) REVERT: B 8 ARG cc_start: 0.7953 (mmp80) cc_final: 0.7709 (mmp80) REVERT: B 49 ARG cc_start: 0.7180 (mpt90) cc_final: 0.6856 (mtt90) REVERT: B 59 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.7364 (t80) REVERT: B 153 ASP cc_start: 0.7625 (m-30) cc_final: 0.7390 (m-30) REVERT: B 258 ASP cc_start: 0.7863 (t70) cc_final: 0.7457 (t70) REVERT: B 314 ARG cc_start: 0.7684 (ptm160) cc_final: 0.7450 (ttt180) REVERT: G 25 ILE cc_start: 0.7965 (OUTLIER) cc_final: 0.7710 (mp) REVERT: G 38 MET cc_start: 0.6055 (ppp) cc_final: 0.5746 (ppp) REVERT: N 80 TYR cc_start: 0.7515 (m-80) cc_final: 0.7250 (m-80) outliers start: 31 outliers final: 23 residues processed: 275 average time/residue: 0.2636 time to fit residues: 92.2711 Evaluate side-chains 289 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 264 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.0670 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 61 optimal weight: 0.0670 chunk 59 optimal weight: 0.2980 chunk 45 optimal weight: 0.0670 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.2394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN A 226 ASN N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7202 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8558 Z= 0.145 Angle : 0.505 11.395 11594 Z= 0.265 Chirality : 0.040 0.161 1317 Planarity : 0.004 0.045 1466 Dihedral : 4.167 18.212 1139 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.84 % Allowed : 19.54 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.26), residues: 1047 helix: 3.00 (0.23), residues: 442 sheet: 0.98 (0.35), residues: 219 loop : -0.75 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 97 HIS 0.004 0.001 HIS A 212 PHE 0.020 0.001 PHE A 77 TYR 0.012 0.001 TYR B 289 ARG 0.008 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 255 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: R 22 PHE cc_start: 0.7073 (t80) cc_final: 0.6847 (t80) REVERT: R 162 MET cc_start: 0.4488 (ptt) cc_final: 0.4161 (ptt) REVERT: R 204 LYS cc_start: 0.8359 (ttmm) cc_final: 0.8142 (ttmm) REVERT: R 207 LYS cc_start: 0.7939 (ttpt) cc_final: 0.7670 (ttpt) REVERT: R 285 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7903 (tmtt) REVERT: A 13 LYS cc_start: 0.7717 (pptt) cc_final: 0.7384 (pptt) REVERT: A 59 LEU cc_start: 0.8288 (tp) cc_final: 0.8071 (tp) REVERT: A 121 LEU cc_start: 0.7726 (tp) cc_final: 0.7464 (mt) REVERT: A 123 GLU cc_start: 0.6961 (tt0) cc_final: 0.6759 (tt0) REVERT: A 146 LEU cc_start: 0.7666 (mp) cc_final: 0.7452 (mp) REVERT: A 195 PHE cc_start: 0.8007 (t80) cc_final: 0.7621 (t80) REVERT: A 202 ARG cc_start: 0.6905 (mtm180) cc_final: 0.6446 (mtm180) REVERT: A 236 ASP cc_start: 0.7585 (t70) cc_final: 0.7260 (t0) REVERT: B 49 ARG cc_start: 0.7139 (mpt90) cc_final: 0.6811 (mtt90) REVERT: B 198 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8287 (pt) REVERT: B 234 PHE cc_start: 0.8767 (OUTLIER) cc_final: 0.8207 (m-80) REVERT: B 258 ASP cc_start: 0.7814 (t70) cc_final: 0.7387 (t70) REVERT: G 25 ILE cc_start: 0.7923 (OUTLIER) cc_final: 0.7599 (mp) REVERT: G 38 MET cc_start: 0.6068 (ppp) cc_final: 0.5734 (ppp) REVERT: N 80 TYR cc_start: 0.7405 (m-80) cc_final: 0.7170 (m-80) REVERT: N 117 TYR cc_start: 0.7814 (m-80) cc_final: 0.7605 (m-80) outliers start: 26 outliers final: 18 residues processed: 262 average time/residue: 0.2704 time to fit residues: 90.0306 Evaluate side-chains 270 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 249 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 0.0010 chunk 55 optimal weight: 0.2980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 184 ASN ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN ** A 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN B 91 HIS N 3 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8558 Z= 0.185 Angle : 0.525 13.783 11594 Z= 0.272 Chirality : 0.041 0.164 1317 Planarity : 0.004 0.045 1466 Dihedral : 4.173 17.981 1139 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.84 % Allowed : 20.31 % Favored : 76.86 % 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: 1.85 (0.26), residues: 1047 helix: 2.96 (0.23), residues: 443 sheet: 0.88 (0.34), residues: 221 loop : -0.70 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.004 0.001 HIS A 212 PHE 0.021 0.001 PHE A 77 TYR 0.011 0.001 TYR B 289 ARG 0.010 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 263 time to evaluate : 0.900 Fit side-chains revert: symmetry clash REVERT: R 22 PHE cc_start: 0.7094 (t80) cc_final: 0.6867 (t80) REVERT: R 162 MET cc_start: 0.4477 (ptt) cc_final: 0.4154 (ptt) REVERT: R 204 LYS cc_start: 0.8379 (ttmm) cc_final: 0.8159 (ttmm) REVERT: R 207 LYS cc_start: 0.7946 (ttpt) cc_final: 0.7675 (ttpt) REVERT: R 285 LYS cc_start: 0.8266 (tmtt) cc_final: 0.7905 (tmtt) REVERT: A 13 LYS cc_start: 0.7728 (pptt) cc_final: 0.7391 (pptt) REVERT: A 59 LEU cc_start: 0.8302 (tp) cc_final: 0.8049 (tp) REVERT: A 121 LEU cc_start: 0.7707 (tp) cc_final: 0.7450 (mt) REVERT: A 123 GLU cc_start: 0.6937 (tt0) cc_final: 0.6692 (tt0) REVERT: A 195 PHE cc_start: 0.8057 (t80) cc_final: 0.7638 (t80) REVERT: A 202 ARG cc_start: 0.6921 (mtm180) cc_final: 0.6471 (mtm180) REVERT: A 236 ASP cc_start: 0.7602 (t70) cc_final: 0.7255 (t0) REVERT: B 8 ARG cc_start: 0.7932 (mmp80) cc_final: 0.7707 (mmp80) REVERT: B 49 ARG cc_start: 0.7159 (mpt90) cc_final: 0.6830 (mtt90) REVERT: B 153 ASP cc_start: 0.7625 (m-30) cc_final: 0.7388 (m-30) REVERT: B 198 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8293 (pt) REVERT: B 234 PHE cc_start: 0.8779 (OUTLIER) cc_final: 0.8242 (m-80) REVERT: B 258 ASP cc_start: 0.7841 (t70) cc_final: 0.7388 (t70) REVERT: G 25 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7594 (mp) REVERT: G 38 MET cc_start: 0.6091 (ppp) cc_final: 0.5758 (ppp) REVERT: N 80 TYR cc_start: 0.7446 (m-80) cc_final: 0.7205 (m-80) outliers start: 26 outliers final: 20 residues processed: 268 average time/residue: 0.2698 time to fit residues: 92.3675 Evaluate side-chains 284 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 221 MET Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 119 ASN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8558 Z= 0.257 Angle : 0.556 13.893 11594 Z= 0.290 Chirality : 0.042 0.168 1317 Planarity : 0.004 0.047 1466 Dihedral : 4.271 18.904 1139 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.73 % Allowed : 21.18 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.26), residues: 1047 helix: 2.88 (0.23), residues: 440 sheet: 0.78 (0.34), residues: 221 loop : -0.73 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.004 0.001 HIS R 205 PHE 0.023 0.002 PHE A 77 TYR 0.017 0.001 TYR A 118 ARG 0.010 0.001 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 263 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 22 PHE cc_start: 0.7112 (t80) cc_final: 0.6883 (t80) REVERT: R 204 LYS cc_start: 0.8402 (ttmm) cc_final: 0.8179 (ttmm) REVERT: R 207 LYS cc_start: 0.7953 (ttpt) cc_final: 0.7678 (ttpt) REVERT: R 285 LYS cc_start: 0.8291 (tmtt) cc_final: 0.7927 (tmtt) REVERT: A 13 LYS cc_start: 0.7735 (pptt) cc_final: 0.7416 (pptt) REVERT: A 59 LEU cc_start: 0.8345 (tp) cc_final: 0.8095 (tp) REVERT: A 121 LEU cc_start: 0.7699 (tp) cc_final: 0.7428 (mt) REVERT: A 123 GLU cc_start: 0.7016 (tt0) cc_final: 0.6778 (tt0) REVERT: A 146 LEU cc_start: 0.7282 (mt) cc_final: 0.7014 (mp) REVERT: A 195 PHE cc_start: 0.8134 (t80) cc_final: 0.7740 (t80) REVERT: A 202 ARG cc_start: 0.6941 (mtm180) cc_final: 0.6497 (mtm180) REVERT: A 236 ASP cc_start: 0.7616 (t70) cc_final: 0.7262 (t0) REVERT: B 8 ARG cc_start: 0.7942 (mmp80) cc_final: 0.7716 (mmp80) REVERT: B 49 ARG cc_start: 0.7196 (mpt90) cc_final: 0.6890 (mtt90) REVERT: B 153 ASP cc_start: 0.7620 (m-30) cc_final: 0.7396 (m-30) REVERT: B 234 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8240 (m-80) REVERT: B 258 ASP cc_start: 0.7866 (t70) cc_final: 0.7399 (t70) REVERT: G 25 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7626 (mp) REVERT: G 38 MET cc_start: 0.6094 (ppp) cc_final: 0.5760 (ppp) REVERT: N 80 TYR cc_start: 0.7460 (m-80) cc_final: 0.7250 (m-80) outliers start: 25 outliers final: 21 residues processed: 269 average time/residue: 0.2685 time to fit residues: 91.6399 Evaluate side-chains 284 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 261 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 221 MET Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.1980 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN B 91 HIS N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8558 Z= 0.212 Angle : 0.542 13.985 11594 Z= 0.282 Chirality : 0.041 0.169 1317 Planarity : 0.004 0.044 1466 Dihedral : 4.240 18.550 1139 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.84 % Allowed : 21.18 % Favored : 75.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1047 helix: 2.92 (0.23), residues: 440 sheet: 0.78 (0.34), residues: 221 loop : -0.74 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.004 0.001 HIS A 212 PHE 0.021 0.001 PHE A 77 TYR 0.011 0.001 TYR B 289 ARG 0.010 0.000 ARG B 68 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2094 Ramachandran restraints generated. 1047 Oldfield, 0 Emsley, 1047 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 262 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 22 PHE cc_start: 0.7100 (t80) cc_final: 0.6871 (t80) REVERT: R 204 LYS cc_start: 0.8397 (ttmm) cc_final: 0.8169 (ttmm) REVERT: R 207 LYS cc_start: 0.7952 (ttpt) cc_final: 0.7676 (ttpt) REVERT: R 285 LYS cc_start: 0.8256 (tmtt) cc_final: 0.7921 (tmtt) REVERT: A 13 LYS cc_start: 0.7725 (pptt) cc_final: 0.7414 (pptt) REVERT: A 59 LEU cc_start: 0.8394 (tp) cc_final: 0.8164 (tp) REVERT: A 76 LYS cc_start: 0.7733 (mtpp) cc_final: 0.7467 (mtpp) REVERT: A 121 LEU cc_start: 0.7712 (tp) cc_final: 0.7419 (mt) REVERT: A 123 GLU cc_start: 0.6994 (tt0) cc_final: 0.6758 (tt0) REVERT: A 146 LEU cc_start: 0.7247 (mt) cc_final: 0.6999 (mp) REVERT: A 195 PHE cc_start: 0.8123 (t80) cc_final: 0.7748 (t80) REVERT: A 202 ARG cc_start: 0.6948 (mtm180) cc_final: 0.6561 (mtm180) REVERT: A 236 ASP cc_start: 0.7603 (t70) cc_final: 0.7237 (t0) REVERT: B 8 ARG cc_start: 0.7934 (mmp80) cc_final: 0.7690 (mmp80) REVERT: B 49 ARG cc_start: 0.7192 (mpt90) cc_final: 0.6867 (mtt90) REVERT: B 153 ASP cc_start: 0.7615 (m-30) cc_final: 0.7390 (m-30) REVERT: B 198 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8301 (pt) REVERT: B 234 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8175 (m-80) REVERT: B 258 ASP cc_start: 0.7801 (t70) cc_final: 0.7404 (t70) REVERT: G 25 ILE cc_start: 0.7938 (OUTLIER) cc_final: 0.7605 (mp) REVERT: G 38 MET cc_start: 0.6114 (ppp) cc_final: 0.5787 (ppp) REVERT: N 80 TYR cc_start: 0.7440 (m-80) cc_final: 0.7232 (m-80) REVERT: N 117 TYR cc_start: 0.7895 (m-80) cc_final: 0.7637 (m-80) outliers start: 26 outliers final: 20 residues processed: 268 average time/residue: 0.2805 time to fit residues: 95.6830 Evaluate side-chains 283 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 260 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 49 THR Chi-restraints excluded: chain R residue 149 MET Chi-restraints excluded: chain R residue 193 ILE Chi-restraints excluded: chain R residue 221 MET Chi-restraints excluded: chain R residue 297 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 4 LEU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.143598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.124162 restraints weight = 12387.377| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 2.35 r_work: 0.3508 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8558 Z= 0.250 Angle : 0.560 13.923 11594 Z= 0.291 Chirality : 0.042 0.173 1317 Planarity : 0.004 0.050 1466 Dihedral : 4.311 19.000 1139 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.73 % Allowed : 21.40 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1047 helix: 2.82 (0.23), residues: 440 sheet: 0.72 (0.35), residues: 221 loop : -0.74 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 339 HIS 0.004 0.001 HIS R 205 PHE 0.024 0.002 PHE A 77 TYR 0.012 0.001 TYR A 194 ARG 0.011 0.001 ARG B 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.53 seconds wall clock time: 48 minutes 22.99 seconds (2902.99 seconds total)