Starting phenix.real_space_refine on Fri Dec 8 12:33:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/12_2023/7xp5_33365.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/12_2023/7xp5_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_33365/12_2023/7xp5_33365.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/12_2023/7xp5_33365.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/12_2023/7xp5_33365.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp5_33365/12_2023/7xp5_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 4.99, per 1000 atoms: 0.60 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: 3.37 Conformation dependent library (CDL) restraints added in 1.7 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: 1.04 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: 2.52 Time building geometry restraints manager: 3.64 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: 0.980 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: 3.930 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.400 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: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.610 ------------------------------------------------------------------------------- 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 : 0.992 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2641 time to fit residues: 94.6314 Evaluate side-chains 265 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 265 time to evaluate : 0.915 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2758 ------------------------------------------------------------------------------- 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: 0.3980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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: 0.7229 moved from start: 0.0964 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= 0.225 Angle : 0.537 6.366 11594 Z= 0.290 Chirality : 0.042 0.145 1317 Planarity : 0.004 0.053 1466 Dihedral : 4.441 19.534 1139 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.20 % Allowed : 12.99 % Favored : 85.81 % 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: 1.78 (0.26), residues: 1047 helix: 2.84 (0.23), residues: 439 sheet: 0.89 (0.35), residues: 219 loop : -0.64 (0.32), residues: 389 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 0.023 0.001 PHE A 77 TYR 0.034 0.002 TYR B 59 ARG 0.007 0.001 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 283 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 272 time to evaluate : 0.936 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 9 residues processed: 273 average time/residue: 0.2751 time to fit residues: 95.5969 Evaluate side-chains 265 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 256 time to evaluate : 1.011 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0848 time to fit residues: 2.9763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0470 chunk 77 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 143 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 176 ASN ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7233 moved from start: 0.1220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8558 Z= 0.227 Angle : 0.530 7.819 11594 Z= 0.282 Chirality : 0.041 0.137 1317 Planarity : 0.004 0.051 1466 Dihedral : 4.391 20.675 1139 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.20 % Allowed : 15.17 % 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: 1.80 (0.26), residues: 1047 helix: 2.90 (0.23), residues: 439 sheet: 0.89 (0.35), residues: 217 loop : -0.67 (0.31), residues: 391 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 0.021 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 283 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 272 time to evaluate : 0.970 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 273 average time/residue: 0.2722 time to fit residues: 94.6387 Evaluate side-chains 270 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 260 time to evaluate : 0.832 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1117 time to fit residues: 3.0965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 0.0060 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.0370 chunk 62 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 55 optimal weight: 0.3980 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 143 HIS R 176 ASN ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8558 Z= 0.164 Angle : 0.502 6.290 11594 Z= 0.267 Chirality : 0.040 0.139 1317 Planarity : 0.004 0.045 1466 Dihedral : 4.246 20.681 1139 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.42 % Allowed : 17.58 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.26), residues: 1047 helix: 3.01 (0.23), residues: 440 sheet: 0.95 (0.35), residues: 217 loop : -0.69 (0.31), residues: 390 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 0.020 0.001 PHE A 77 TYR 0.018 0.001 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 286 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 273 time to evaluate : 0.950 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 279 average time/residue: 0.2725 time to fit residues: 96.4591 Evaluate side-chains 266 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 258 time to evaluate : 0.934 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0883 time to fit residues: 2.6625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 B 239 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1575 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= 0.250 Angle : 0.541 7.734 11594 Z= 0.285 Chirality : 0.041 0.142 1317 Planarity : 0.004 0.045 1466 Dihedral : 4.363 21.116 1139 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.98 % Allowed : 18.34 % Favored : 80.68 % 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: 1.77 (0.26), residues: 1047 helix: 2.90 (0.23), residues: 440 sheet: 0.76 (0.34), residues: 219 loop : -0.67 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 99 HIS 0.004 0.001 HIS R 205 PHE 0.016 0.001 PHE B 235 TYR 0.013 0.001 TYR N 80 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 283 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 274 time to evaluate : 1.005 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 278 average time/residue: 0.2737 time to fit residues: 96.8508 Evaluate side-chains 271 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 265 time to evaluate : 0.829 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0779 time to fit residues: 2.0271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 51 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8558 Z= 0.259 Angle : 0.555 8.249 11594 Z= 0.292 Chirality : 0.042 0.141 1317 Planarity : 0.004 0.045 1466 Dihedral : 4.402 21.514 1139 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.53 % Allowed : 19.65 % Favored : 78.82 % 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: 1.64 (0.26), residues: 1047 helix: 2.73 (0.23), residues: 446 sheet: 0.69 (0.34), residues: 219 loop : -0.70 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 339 HIS 0.004 0.001 HIS R 205 PHE 0.020 0.001 PHE A 195 TYR 0.013 0.001 TYR N 80 ARG 0.008 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 282 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 268 time to evaluate : 0.944 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 272 average time/residue: 0.2885 time to fit residues: 99.3330 Evaluate side-chains 270 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 263 time to evaluate : 0.972 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0928 time to fit residues: 2.4437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 98 optimal weight: 0.0050 chunk 61 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 119 ASN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8558 Z= 0.202 Angle : 0.540 7.826 11594 Z= 0.284 Chirality : 0.041 0.144 1317 Planarity : 0.004 0.044 1466 Dihedral : 4.308 22.112 1139 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.76 % Allowed : 21.18 % Favored : 78.06 % 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: 1.68 (0.26), residues: 1047 helix: 2.75 (0.23), residues: 449 sheet: 0.77 (0.35), residues: 219 loop : -0.74 (0.31), residues: 379 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 0.018 0.001 PHE A 77 TYR 0.013 0.001 TYR N 80 ARG 0.008 0.000 ARG A 188 *********************** 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 261 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 254 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 258 average time/residue: 0.2877 time to fit residues: 93.3738 Evaluate side-chains 254 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 250 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0793 time to fit residues: 1.7831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 66 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 0.0980 chunk 55 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 ASN ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS N 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8558 Z= 0.202 Angle : 0.545 8.229 11594 Z= 0.287 Chirality : 0.041 0.154 1317 Planarity : 0.004 0.044 1466 Dihedral : 4.279 19.489 1139 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.76 % Allowed : 22.38 % 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: 1.69 (0.26), residues: 1047 helix: 2.80 (0.23), residues: 448 sheet: 0.73 (0.35), residues: 225 loop : -0.76 (0.31), residues: 374 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 0.026 0.001 PHE A 77 TYR 0.014 0.001 TYR N 80 ARG 0.008 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 265 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 258 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 260 average time/residue: 0.2941 time to fit residues: 96.3347 Evaluate side-chains 262 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 257 time to evaluate : 0.942 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0797 time to fit residues: 2.0912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.0980 chunk 71 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 60 optimal weight: 0.0770 chunk 96 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 67 optimal weight: 0.5980 overall best weight: 0.2938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8558 Z= 0.163 Angle : 0.531 9.128 11594 Z= 0.278 Chirality : 0.040 0.151 1317 Planarity : 0.004 0.045 1466 Dihedral : 4.166 17.704 1139 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.33 % Allowed : 22.82 % 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: 1.84 (0.26), residues: 1047 helix: 3.03 (0.23), residues: 444 sheet: 0.87 (0.35), residues: 222 loop : -0.83 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP R 97 HIS 0.004 0.001 HIS A 212 PHE 0.033 0.001 PHE A 77 TYR 0.013 0.001 TYR N 80 ARG 0.008 0.000 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 267 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 264 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 264 average time/residue: 0.2966 time to fit residues: 98.8692 Evaluate side-chains 265 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 263 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0783 time to fit residues: 1.5941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 64 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 78 GLN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8558 Z= 0.222 Angle : 0.564 8.298 11594 Z= 0.295 Chirality : 0.041 0.171 1317 Planarity : 0.004 0.044 1466 Dihedral : 4.268 19.373 1139 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.44 % Allowed : 23.47 % 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: 1.75 (0.26), residues: 1047 helix: 2.91 (0.23), residues: 444 sheet: 0.74 (0.35), residues: 224 loop : -0.76 (0.32), residues: 379 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 0.038 0.001 PHE A 77 TYR 0.014 0.001 TYR N 80 ARG 0.009 0.001 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 259 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 255 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 255 average time/residue: 0.3049 time to fit residues: 98.8519 Evaluate side-chains 258 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 255 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1042 time to fit residues: 1.9462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.141457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122253 restraints weight = 12464.989| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.24 r_work: 0.3493 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8558 Z= 0.294 Angle : 0.609 11.580 11594 Z= 0.317 Chirality : 0.043 0.175 1317 Planarity : 0.004 0.048 1466 Dihedral : 4.457 20.178 1139 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.33 % Allowed : 24.02 % Favored : 75.66 % 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: 1.55 (0.26), residues: 1047 helix: 2.73 (0.23), residues: 441 sheet: 0.59 (0.35), residues: 225 loop : -0.78 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 339 HIS 0.004 0.001 HIS R 205 PHE 0.035 0.002 PHE A 77 TYR 0.015 0.002 TYR N 80 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: 2751.02 seconds wall clock time: 49 minutes 52.97 seconds (2992.97 seconds total)