Starting phenix.real_space_refine on Fri Jul 19 15:48:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp4_33364/07_2024/7xp4_33364.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp4_33364/07_2024/7xp4_33364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp4_33364/07_2024/7xp4_33364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp4_33364/07_2024/7xp4_33364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp4_33364/07_2024/7xp4_33364.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xp4_33364/07_2024/7xp4_33364.cif" } resolution = 3.01 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 49 5.16 5 C 5382 2.51 5 N 1456 2.21 5 O 1550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "N PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 8437 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1964 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} 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: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 981 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "R" Number of atoms: 2440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2440 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 8, 'TRANS': 290} Time building chain proxies: 5.05, per 1000 atoms: 0.60 Number of scatterers: 8437 At special positions: 0 Unit cell: (83.2, 101.92, 134.16, 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 49 16.00 O 1550 8.00 N 1456 7.00 C 5382 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 97 " distance=2.03 Simple disulfide: pdb=" SG CYS N 100 " - pdb=" SG CYS N 108 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.16 Conformation dependent library (CDL) restraints added in 1.7 seconds 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2008 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 10 sheets defined 45.5% alpha, 19.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 5 through 36 Processing helix chain 'A' and resid 48 through 60 removed outlier: 3.562A pdb=" N LEU A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N HIS A 60 " --> pdb=" O MET A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 117 through 133 removed outlier: 4.072A pdb=" N GLN A 122 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLU A 123 " --> pdb=" O ASN A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 138 removed outlier: 3.784A pdb=" N ARG A 138 " --> pdb=" O ARG A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 159 Processing helix chain 'A' and resid 162 through 167 removed outlier: 4.214A pdb=" N TYR A 166 " --> pdb=" O LYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 206 Processing helix chain 'A' and resid 222 through 247 removed outlier: 3.967A pdb=" N ASN A 226 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 37 removed outlier: 4.111A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.702A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.774A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 63 through 66 Processing helix chain 'N' and resid 88 through 92 Processing helix chain 'R' and resid 4 through 39 removed outlier: 4.814A pdb=" N SER R 10 " --> pdb=" O PRO R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 70 Processing helix chain 'R' and resid 77 through 111 removed outlier: 3.584A pdb=" N ILE R 82 " --> pdb=" O ILE R 78 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N PHE R 94 " --> pdb=" O VAL R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 124 removed outlier: 4.103A pdb=" N ARG R 124 " --> pdb=" O HIS R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 124 through 151 removed outlier: 3.615A pdb=" N VAL R 128 " --> pdb=" O ARG R 124 " (cutoff:3.500A) Proline residue: R 136 - end of helix removed outlier: 3.643A pdb=" N PHE R 139 " --> pdb=" O GLY R 135 " (cutoff:3.500A) Processing helix chain 'R' and resid 155 through 160 Processing helix chain 'R' and resid 176 through 213 removed outlier: 4.864A pdb=" N VAL R 186 " --> pdb=" O LEU R 182 " (cutoff:3.500A) Proline residue: R 187 - end of helix removed outlier: 3.933A pdb=" N HIS R 212 " --> pdb=" O LYS R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 250 Processing helix chain 'R' and resid 257 through 283 removed outlier: 3.934A pdb=" N PHE R 263 " --> pdb=" O PRO R 259 " (cutoff:3.500A) Proline residue: R 272 - end of helix Proline residue: R 276 - end of helix Processing helix chain 'R' and resid 283 through 301 Processing sheet with id=AA1, first strand: chain 'A' and resid 72 through 79 removed outlier: 4.609A pdb=" N VAL A 89 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N GLY A 43 " --> pdb=" O VAL A 89 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N ARG A 38 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N ILE A 110 " --> pdb=" O ARG A 38 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N LEU A 40 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N VAL A 112 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU A 42 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 8.681A pdb=" N ASP A 114 " --> pdb=" O LEU A 42 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ILE A 109 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N PHE A 145 " --> pdb=" O ILE A 109 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N PHE A 111 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ASN A 147 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N VAL A 113 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N VAL A 142 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS A 217 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 144 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 45 through 51 removed outlier: 5.779A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 3.762A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN B 88 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 103 through 105 removed outlier: 6.377A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.506A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.722A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.278A 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: 3.571A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.110A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 4 through 7 removed outlier: 3.541A pdb=" N GLN N 6 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 12 through 13 removed outlier: 7.160A pdb=" N MET N 35 " --> pdb=" O ASP N 51 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ASP N 51 " --> pdb=" O MET N 35 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP N 37 " --> pdb=" O VAL N 49 " (cutoff:3.500A) 463 hydrogen bonds defined for protein. 1338 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: 2.46 Time building geometry restraints manager: 3.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2722 1.34 - 1.46: 1493 1.46 - 1.58: 4332 1.58 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8617 Sorted by residual: bond pdb=" N GLY B 341 " pdb=" CA GLY B 341 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.05e-02 9.07e+03 1.60e+01 bond pdb=" N SER B 342 " pdb=" CA SER B 342 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.21e-02 6.83e+03 6.15e+00 bond pdb=" N ASN B 340 " pdb=" CA ASN B 340 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.20e-02 6.94e+03 5.36e+00 bond pdb=" CA SER B 342 " pdb=" CB SER B 342 " ideal model delta sigma weight residual 1.531 1.506 0.024 1.52e-02 4.33e+03 2.52e+00 bond pdb=" CA GLY B 341 " pdb=" C GLY B 341 " ideal model delta sigma weight residual 1.519 1.532 -0.013 9.70e-03 1.06e+04 1.86e+00 ... (remaining 8612 not shown) Histogram of bond angle deviations from ideal: 99.38 - 106.31: 159 106.31 - 113.24: 4736 113.24 - 120.17: 2988 120.17 - 127.10: 3695 127.10 - 134.03: 95 Bond angle restraints: 11673 Sorted by residual: angle pdb=" CA GLY B 341 " pdb=" C GLY B 341 " pdb=" O GLY B 341 " ideal model delta sigma weight residual 121.41 118.27 3.14 8.80e-01 1.29e+00 1.27e+01 angle pdb=" C ASP B 118 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " ideal model delta sigma weight residual 121.54 128.23 -6.69 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C LYS R 167 " pdb=" N LEU R 168 " pdb=" CA LEU R 168 " ideal model delta sigma weight residual 122.42 118.04 4.38 1.55e+00 4.16e-01 7.99e+00 angle pdb=" C LYS A 98 " pdb=" N TRP A 99 " pdb=" CA TRP A 99 " ideal model delta sigma weight residual 121.14 116.33 4.81 1.75e+00 3.27e-01 7.57e+00 angle pdb=" C GLY A 159 " pdb=" N LYS A 160 " pdb=" CA LYS A 160 " ideal model delta sigma weight residual 121.54 126.42 -4.88 1.91e+00 2.74e-01 6.52e+00 ... (remaining 11668 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 4678 17.58 - 35.15: 369 35.15 - 52.73: 60 52.73 - 70.30: 3 70.30 - 87.88: 4 Dihedral angle restraints: 5114 sinusoidal: 2015 harmonic: 3099 Sorted by residual: dihedral pdb=" CA CYS N 108 " pdb=" C CYS N 108 " pdb=" N PHE N 109 " pdb=" CA PHE N 109 " ideal model delta harmonic sigma weight residual -180.00 -161.16 -18.84 0 5.00e+00 4.00e-02 1.42e+01 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 180.00 162.63 17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CB CYS N 100 " pdb=" SG CYS N 100 " pdb=" SG CYS N 108 " pdb=" CB CYS N 108 " ideal model delta sinusoidal sigma weight residual 93.00 66.09 26.91 1 1.00e+01 1.00e-02 1.04e+01 ... (remaining 5111 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 836 0.033 - 0.066: 323 0.066 - 0.099: 105 0.099 - 0.132: 54 0.132 - 0.165: 4 Chirality restraints: 1322 Sorted by residual: chirality pdb=" CB THR B 47 " pdb=" CA THR B 47 " pdb=" OG1 THR B 47 " pdb=" CG2 THR B 47 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CA TRP A 99 " pdb=" N TRP A 99 " pdb=" C TRP A 99 " pdb=" CB TRP A 99 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.55e-01 chirality pdb=" CG LEU R 168 " pdb=" CB LEU R 168 " pdb=" CD1 LEU R 168 " pdb=" CD2 LEU R 168 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 5.02e-01 ... (remaining 1319 not shown) Planarity restraints: 1475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.061 5.00e-02 4.00e+02 9.21e-02 1.36e+01 pdb=" N PRO G 60 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 186 " 0.040 5.00e-02 4.00e+02 6.03e-02 5.81e+00 pdb=" N PRO A 187 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP R 218 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.15e+00 pdb=" N PRO R 219 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO R 219 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 219 " -0.025 5.00e-02 4.00e+02 ... (remaining 1472 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 849 2.74 - 3.28: 8437 3.28 - 3.82: 14068 3.82 - 4.36: 15810 4.36 - 4.90: 28449 Nonbonded interactions: 67613 Sorted by model distance: nonbonded pdb=" O VAL N 111 " pdb=" OG1 THR N 112 " model vdw 2.204 2.440 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.209 2.440 nonbonded pdb=" OG SER R 244 " pdb=" O CYS R 264 " model vdw 2.240 2.440 nonbonded pdb=" OD1 ASN R 31 " pdb=" NZ LYS R 285 " model vdw 2.250 2.520 nonbonded pdb=" O ALA A 44 " pdb=" OG SER A 47 " model vdw 2.252 2.440 ... (remaining 67608 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.240 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.730 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 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 : 0.003 0.042 8617 Z= 0.221 Angle : 0.577 8.735 11673 Z= 0.311 Chirality : 0.043 0.165 1322 Planarity : 0.005 0.092 1475 Dihedral : 12.473 87.879 3100 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.94 % Favored : 96.96 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.26), residues: 1054 helix: 2.11 (0.24), residues: 437 sheet: 0.12 (0.34), residues: 227 loop : -0.91 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP R 66 HIS 0.003 0.001 HIS A 212 PHE 0.023 0.001 PHE R 9 TYR 0.011 0.001 TYR B 59 ARG 0.014 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 259 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 LYS cc_start: 0.6997 (tptp) cc_final: 0.6764 (tptp) REVERT: A 23 GLU cc_start: 0.7301 (tp30) cc_final: 0.6910 (tp30) REVERT: A 29 ASP cc_start: 0.6665 (t0) cc_final: 0.6404 (t0) REVERT: A 42 LEU cc_start: 0.7911 (mt) cc_final: 0.7696 (mt) REVERT: A 74 GLU cc_start: 0.7137 (pt0) cc_final: 0.6769 (pt0) REVERT: A 103 PHE cc_start: 0.7741 (m-10) cc_final: 0.7518 (m-80) REVERT: A 117 ASP cc_start: 0.6723 (m-30) cc_final: 0.6262 (m-30) REVERT: A 123 GLU cc_start: 0.6958 (pt0) cc_final: 0.5993 (pt0) REVERT: A 241 GLU cc_start: 0.6535 (mt-10) cc_final: 0.6303 (mt-10) REVERT: B 25 CYS cc_start: 0.7178 (m) cc_final: 0.6676 (m) REVERT: B 135 VAL cc_start: 0.8461 (t) cc_final: 0.8203 (p) REVERT: B 245 SER cc_start: 0.7960 (p) cc_final: 0.7547 (p) REVERT: G 13 ARG cc_start: 0.7198 (tmt-80) cc_final: 0.6615 (tmt-80) REVERT: R 207 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7540 (tmtt) REVERT: R 250 TRP cc_start: 0.7126 (p-90) cc_final: 0.6650 (p-90) REVERT: R 262 MET cc_start: 0.6038 (ppp) cc_final: 0.5696 (ppp) REVERT: R 284 LYS cc_start: 0.7464 (tptp) cc_final: 0.7083 (tptp) outliers start: 0 outliers final: 0 residues processed: 259 average time/residue: 0.2771 time to fit residues: 91.3838 Evaluate side-chains 242 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 242 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 94 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN B 155 ASN B 220 GLN B 340 ASN G 59 ASN N 40 GLN N 85 ASN R 65 ASN R 176 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8617 Z= 0.233 Angle : 0.560 6.818 11673 Z= 0.299 Chirality : 0.042 0.178 1322 Planarity : 0.004 0.067 1475 Dihedral : 4.153 19.792 1147 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.41 % Allowed : 10.40 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1054 helix: 2.26 (0.24), residues: 451 sheet: 0.26 (0.35), residues: 219 loop : -0.95 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 99 HIS 0.003 0.001 HIS A 212 PHE 0.023 0.001 PHE R 9 TYR 0.010 0.001 TYR A 194 ARG 0.005 0.000 ARG B 251 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 261 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: A 20 LYS cc_start: 0.6976 (tptp) cc_final: 0.6754 (tptp) REVERT: A 23 GLU cc_start: 0.7279 (tp30) cc_final: 0.6893 (tp30) REVERT: A 29 ASP cc_start: 0.6757 (t0) cc_final: 0.6500 (t0) REVERT: A 42 LEU cc_start: 0.7925 (mt) cc_final: 0.7718 (mt) REVERT: A 74 GLU cc_start: 0.7082 (pt0) cc_final: 0.6744 (pt0) REVERT: A 123 GLU cc_start: 0.6819 (pt0) cc_final: 0.6346 (pt0) REVERT: A 241 GLU cc_start: 0.6539 (mt-10) cc_final: 0.6320 (mt-10) REVERT: B 96 ARG cc_start: 0.6433 (mmp80) cc_final: 0.6204 (mmp80) REVERT: G 13 ARG cc_start: 0.7244 (tmt-80) cc_final: 0.6651 (tmt-80) REVERT: N 61 TYR cc_start: 0.7815 (m-80) cc_final: 0.7447 (m-80) REVERT: R 112 ASN cc_start: 0.8570 (p0) cc_final: 0.8365 (p0) REVERT: R 145 PHE cc_start: 0.7826 (t80) cc_final: 0.7620 (t80) REVERT: R 207 LYS cc_start: 0.7615 (tmtt) cc_final: 0.7377 (tmtt) REVERT: R 250 TRP cc_start: 0.6883 (p-90) cc_final: 0.6563 (p-90) REVERT: R 262 MET cc_start: 0.6168 (ppp) cc_final: 0.5926 (ppp) REVERT: R 284 LYS cc_start: 0.7676 (tptp) cc_final: 0.7273 (tptp) outliers start: 13 outliers final: 9 residues processed: 263 average time/residue: 0.2511 time to fit residues: 85.7563 Evaluate side-chains 253 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 244 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 267 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 94 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 ASN B 266 HIS G 59 ASN R 31 ASN R 86 ASN R 148 ASN R 176 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8617 Z= 0.241 Angle : 0.542 6.306 11673 Z= 0.287 Chirality : 0.041 0.143 1322 Planarity : 0.004 0.057 1475 Dihedral : 4.169 22.178 1147 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.17 % Allowed : 15.17 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.26), residues: 1054 helix: 2.29 (0.24), residues: 451 sheet: 0.28 (0.35), residues: 219 loop : -0.99 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 99 HIS 0.003 0.001 HIS A 212 PHE 0.022 0.001 PHE R 9 TYR 0.011 0.001 TYR A 194 ARG 0.008 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 250 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7258 (tp30) cc_final: 0.6902 (tp30) REVERT: A 29 ASP cc_start: 0.6800 (t0) cc_final: 0.6567 (t0) REVERT: A 123 GLU cc_start: 0.6752 (pt0) cc_final: 0.6454 (pt0) REVERT: A 241 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6326 (mt-10) REVERT: B 118 ASP cc_start: 0.6837 (t70) cc_final: 0.6298 (t0) REVERT: B 173 THR cc_start: 0.8014 (t) cc_final: 0.7737 (p) REVERT: B 188 MET cc_start: 0.7217 (OUTLIER) cc_final: 0.6800 (mmm) REVERT: B 197 ARG cc_start: 0.7080 (mmm160) cc_final: 0.6733 (mmm160) REVERT: G 13 ARG cc_start: 0.7217 (tmt-80) cc_final: 0.6667 (tmt-80) REVERT: N 60 SER cc_start: 0.7804 (m) cc_final: 0.7296 (p) REVERT: R 112 ASN cc_start: 0.8606 (p0) cc_final: 0.8389 (p0) REVERT: R 145 PHE cc_start: 0.7798 (t80) cc_final: 0.7594 (t80) REVERT: R 207 LYS cc_start: 0.7705 (tmtt) cc_final: 0.7451 (tmtt) REVERT: R 250 TRP cc_start: 0.6917 (p-90) cc_final: 0.6595 (p-90) REVERT: R 262 MET cc_start: 0.6292 (ppp) cc_final: 0.5978 (ppp) REVERT: R 284 LYS cc_start: 0.7715 (tptp) cc_final: 0.7262 (tptp) outliers start: 20 outliers final: 13 residues processed: 257 average time/residue: 0.2583 time to fit residues: 85.8480 Evaluate side-chains 254 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 240 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 94 ASP Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 267 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 0.3980 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 8.9990 chunk 89 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 HIS R 176 ASN R 224 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8617 Z= 0.220 Angle : 0.529 7.640 11673 Z= 0.280 Chirality : 0.041 0.155 1322 Planarity : 0.004 0.051 1475 Dihedral : 4.109 19.723 1147 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.60 % Allowed : 16.68 % Favored : 80.72 % 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: 1.12 (0.26), residues: 1054 helix: 2.35 (0.24), residues: 452 sheet: 0.31 (0.35), residues: 218 loop : -0.99 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 99 HIS 0.003 0.001 HIS A 212 PHE 0.022 0.001 PHE R 9 TYR 0.011 0.001 TYR A 194 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 243 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7276 (tp30) cc_final: 0.6888 (tp30) REVERT: A 29 ASP cc_start: 0.6927 (t0) cc_final: 0.6587 (t0) REVERT: A 57 ARG cc_start: 0.7685 (tpp80) cc_final: 0.7373 (tpp80) REVERT: A 123 GLU cc_start: 0.6739 (pt0) cc_final: 0.6476 (pt0) REVERT: A 241 GLU cc_start: 0.6544 (mt-10) cc_final: 0.6326 (mt-10) REVERT: B 197 ARG cc_start: 0.7082 (mmm160) cc_final: 0.6741 (mmm160) REVERT: B 256 ARG cc_start: 0.8277 (ptp-110) cc_final: 0.7920 (mtm-85) REVERT: N 60 SER cc_start: 0.7784 (m) cc_final: 0.7410 (p) REVERT: R 109 LYS cc_start: 0.7601 (mmmm) cc_final: 0.7133 (mmmm) REVERT: R 112 ASN cc_start: 0.8622 (p0) cc_final: 0.8392 (p0) REVERT: R 207 LYS cc_start: 0.7716 (tmtt) cc_final: 0.7445 (tmtt) REVERT: R 247 MET cc_start: 0.7129 (ppp) cc_final: 0.6443 (ppp) REVERT: R 250 TRP cc_start: 0.6832 (p-90) cc_final: 0.6530 (p-90) REVERT: R 262 MET cc_start: 0.6216 (ppp) cc_final: 0.5940 (ppp) REVERT: R 284 LYS cc_start: 0.7739 (tptp) cc_final: 0.7264 (tptp) REVERT: R 287 LYS cc_start: 0.7624 (tppp) cc_final: 0.7192 (tppp) outliers start: 24 outliers final: 19 residues processed: 253 average time/residue: 0.2612 time to fit residues: 84.9340 Evaluate side-chains 250 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 231 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 246 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 267 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 51 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8617 Z= 0.260 Angle : 0.551 10.818 11673 Z= 0.289 Chirality : 0.042 0.144 1322 Planarity : 0.004 0.049 1475 Dihedral : 4.162 18.035 1147 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.12 % Allowed : 17.44 % Favored : 78.44 % 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: 1.05 (0.26), residues: 1054 helix: 2.30 (0.24), residues: 452 sheet: 0.34 (0.35), residues: 218 loop : -1.07 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 99 HIS 0.003 0.001 HIS A 212 PHE 0.022 0.001 PHE R 9 TYR 0.011 0.001 TYR A 194 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 235 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7285 (tp30) cc_final: 0.6926 (tp30) REVERT: A 29 ASP cc_start: 0.6955 (t0) cc_final: 0.6586 (t0) REVERT: A 57 ARG cc_start: 0.7728 (tpp80) cc_final: 0.7437 (tpp80) REVERT: A 123 GLU cc_start: 0.6757 (pt0) cc_final: 0.6511 (pt0) REVERT: A 241 GLU cc_start: 0.6541 (mt-10) cc_final: 0.6329 (mt-10) REVERT: N 60 SER cc_start: 0.7809 (m) cc_final: 0.7428 (p) REVERT: N 109 PHE cc_start: 0.7671 (OUTLIER) cc_final: 0.7320 (m-80) REVERT: R 109 LYS cc_start: 0.7594 (mmmm) cc_final: 0.7116 (mmmm) REVERT: R 112 ASN cc_start: 0.8639 (p0) cc_final: 0.8411 (p0) REVERT: R 207 LYS cc_start: 0.7763 (tmtt) cc_final: 0.7458 (tmtt) REVERT: R 247 MET cc_start: 0.7141 (ppp) cc_final: 0.6594 (ppp) REVERT: R 250 TRP cc_start: 0.6810 (p-90) cc_final: 0.6527 (p-90) REVERT: R 262 MET cc_start: 0.6179 (ppp) cc_final: 0.5915 (ppp) REVERT: R 284 LYS cc_start: 0.7756 (tptp) cc_final: 0.7309 (tptp) REVERT: R 287 LYS cc_start: 0.7645 (tppp) cc_final: 0.7261 (tppp) outliers start: 38 outliers final: 25 residues processed: 255 average time/residue: 0.2532 time to fit residues: 83.2932 Evaluate side-chains 264 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 238 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 85 ASN Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 246 ILE Chi-restraints excluded: chain R residue 267 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 97 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN A 147 ASN B 88 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7220 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8617 Z= 0.245 Angle : 0.551 12.714 11673 Z= 0.287 Chirality : 0.041 0.142 1322 Planarity : 0.004 0.049 1475 Dihedral : 4.148 21.382 1147 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.36 % Allowed : 18.96 % Favored : 77.68 % 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: 1.10 (0.26), residues: 1054 helix: 2.36 (0.24), residues: 452 sheet: 0.35 (0.35), residues: 218 loop : -1.07 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 99 HIS 0.003 0.001 HIS A 212 PHE 0.022 0.001 PHE R 9 TYR 0.011 0.001 TYR A 194 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 235 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7288 (tp30) cc_final: 0.6925 (tp30) REVERT: A 29 ASP cc_start: 0.6952 (t0) cc_final: 0.6584 (t0) REVERT: A 55 GLN cc_start: 0.6960 (OUTLIER) cc_final: 0.6698 (tt0) REVERT: A 123 GLU cc_start: 0.6742 (pt0) cc_final: 0.6521 (pt0) REVERT: A 241 GLU cc_start: 0.6540 (mt-10) cc_final: 0.6327 (mt-10) REVERT: B 256 ARG cc_start: 0.8251 (ptp-110) cc_final: 0.7864 (mtm-85) REVERT: N 60 SER cc_start: 0.7815 (m) cc_final: 0.7427 (p) REVERT: N 109 PHE cc_start: 0.7712 (OUTLIER) cc_final: 0.7338 (m-80) REVERT: R 109 LYS cc_start: 0.7580 (mmmm) cc_final: 0.7069 (mmmm) REVERT: R 112 ASN cc_start: 0.8624 (p0) cc_final: 0.8387 (p0) REVERT: R 207 LYS cc_start: 0.7750 (tmtt) cc_final: 0.7452 (tmtt) REVERT: R 247 MET cc_start: 0.7127 (ppp) cc_final: 0.6696 (ppp) REVERT: R 262 MET cc_start: 0.6130 (ppp) cc_final: 0.5845 (ppp) REVERT: R 284 LYS cc_start: 0.7756 (tptp) cc_final: 0.7329 (tptp) REVERT: R 287 LYS cc_start: 0.7670 (tppp) cc_final: 0.7355 (tppp) outliers start: 31 outliers final: 23 residues processed: 250 average time/residue: 0.2626 time to fit residues: 84.8825 Evaluate side-chains 259 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 234 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 36 THR Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 85 ASN Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 267 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9990 chunk 57 optimal weight: 0.0470 chunk 73 optimal weight: 0.0050 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 100 optimal weight: 0.0170 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 59 optimal weight: 0.6980 overall best weight: 0.2730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN B 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8617 Z= 0.149 Angle : 0.528 12.379 11673 Z= 0.275 Chirality : 0.040 0.135 1322 Planarity : 0.004 0.048 1475 Dihedral : 3.951 20.369 1147 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.93 % Allowed : 20.69 % Favored : 76.38 % 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: 1.27 (0.26), residues: 1054 helix: 2.50 (0.24), residues: 455 sheet: 0.37 (0.35), residues: 218 loop : -0.97 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 99 HIS 0.002 0.001 HIS A 212 PHE 0.024 0.001 PHE R 9 TYR 0.007 0.001 TYR A 194 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 231 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7270 (tp30) cc_final: 0.6929 (tp30) REVERT: A 42 LEU cc_start: 0.7811 (mt) cc_final: 0.7579 (mt) REVERT: A 55 GLN cc_start: 0.6976 (OUTLIER) cc_final: 0.6684 (tt0) REVERT: A 123 GLU cc_start: 0.6719 (pt0) cc_final: 0.6499 (pt0) REVERT: A 241 GLU cc_start: 0.6481 (mt-10) cc_final: 0.6280 (mt-10) REVERT: N 60 SER cc_start: 0.7781 (m) cc_final: 0.7444 (p) REVERT: N 109 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.7302 (m-80) REVERT: R 109 LYS cc_start: 0.7504 (mmmm) cc_final: 0.7129 (mmmm) REVERT: R 112 ASN cc_start: 0.8584 (p0) cc_final: 0.8360 (p0) REVERT: R 207 LYS cc_start: 0.7761 (tmtt) cc_final: 0.7447 (tmtt) REVERT: R 247 MET cc_start: 0.7018 (ppp) cc_final: 0.6421 (ppp) REVERT: R 262 MET cc_start: 0.6043 (ppp) cc_final: 0.5769 (ppp) REVERT: R 280 ILE cc_start: 0.7911 (mt) cc_final: 0.7689 (tt) REVERT: R 284 LYS cc_start: 0.7681 (tptp) cc_final: 0.7229 (tptp) REVERT: R 287 LYS cc_start: 0.7649 (tppp) cc_final: 0.7396 (tppp) outliers start: 27 outliers final: 18 residues processed: 243 average time/residue: 0.2670 time to fit residues: 83.6125 Evaluate side-chains 245 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 225 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 218 ASP Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 267 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 96 optimal weight: 0.2980 chunk 87 optimal weight: 0.7980 chunk 93 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: ** A 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8617 Z= 0.222 Angle : 0.572 14.360 11673 Z= 0.292 Chirality : 0.041 0.136 1322 Planarity : 0.004 0.047 1475 Dihedral : 4.059 20.552 1147 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.60 % Allowed : 21.56 % Favored : 75.84 % 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: 1.20 (0.26), residues: 1054 helix: 2.45 (0.24), residues: 453 sheet: 0.40 (0.35), residues: 220 loop : -1.04 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 99 HIS 0.003 0.001 HIS A 212 PHE 0.023 0.001 PHE R 9 TYR 0.011 0.001 TYR A 194 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 225 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7310 (tp30) cc_final: 0.6955 (tp30) REVERT: A 29 ASP cc_start: 0.7080 (t0) cc_final: 0.6852 (m-30) REVERT: A 55 GLN cc_start: 0.6979 (OUTLIER) cc_final: 0.6701 (tt0) REVERT: A 123 GLU cc_start: 0.6762 (pt0) cc_final: 0.6539 (pt0) REVERT: A 198 ASP cc_start: 0.7189 (t0) cc_final: 0.6851 (m-30) REVERT: A 241 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6317 (mt-10) REVERT: N 60 SER cc_start: 0.7777 (m) cc_final: 0.7438 (p) REVERT: N 109 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7371 (m-80) REVERT: R 109 LYS cc_start: 0.7545 (mmmm) cc_final: 0.7175 (mmmm) REVERT: R 112 ASN cc_start: 0.8625 (p0) cc_final: 0.8402 (p0) REVERT: R 207 LYS cc_start: 0.7767 (tmtt) cc_final: 0.7453 (tmtt) REVERT: R 247 MET cc_start: 0.7050 (ppp) cc_final: 0.6668 (ppp) REVERT: R 262 MET cc_start: 0.6081 (ppp) cc_final: 0.5811 (ppp) REVERT: R 280 ILE cc_start: 0.7946 (mt) cc_final: 0.7734 (mt) REVERT: R 284 LYS cc_start: 0.7777 (tptp) cc_final: 0.7356 (tptp) REVERT: R 287 LYS cc_start: 0.7654 (tppp) cc_final: 0.7401 (tppp) outliers start: 24 outliers final: 20 residues processed: 238 average time/residue: 0.2566 time to fit residues: 79.8025 Evaluate side-chains 243 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 221 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 267 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 chunk 88 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 98 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 ASN A 126 ASN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8617 Z= 0.244 Angle : 0.581 14.139 11673 Z= 0.298 Chirality : 0.041 0.139 1322 Planarity : 0.004 0.047 1475 Dihedral : 4.118 20.921 1147 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.82 % Allowed : 21.56 % Favored : 75.62 % 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: 1.15 (0.26), residues: 1054 helix: 2.44 (0.24), residues: 452 sheet: 0.34 (0.35), residues: 220 loop : -1.07 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 99 HIS 0.003 0.001 HIS A 212 PHE 0.023 0.002 PHE R 9 TYR 0.011 0.001 TYR N 61 ARG 0.010 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 227 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7304 (tp30) cc_final: 0.6970 (tp30) REVERT: A 55 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6726 (tt0) REVERT: A 96 ARG cc_start: 0.7208 (ptt180) cc_final: 0.6983 (ptt180) REVERT: A 123 GLU cc_start: 0.6784 (pt0) cc_final: 0.6558 (pt0) REVERT: A 198 ASP cc_start: 0.7200 (t0) cc_final: 0.6877 (m-30) REVERT: A 241 GLU cc_start: 0.6529 (mt-10) cc_final: 0.6320 (mt-10) REVERT: N 60 SER cc_start: 0.7778 (m) cc_final: 0.7442 (p) REVERT: N 109 PHE cc_start: 0.7744 (OUTLIER) cc_final: 0.7369 (m-80) REVERT: R 109 LYS cc_start: 0.7555 (mmmm) cc_final: 0.7199 (mmmm) REVERT: R 112 ASN cc_start: 0.8627 (p0) cc_final: 0.8373 (p0) REVERT: R 207 LYS cc_start: 0.7752 (tmtt) cc_final: 0.7455 (tmtt) REVERT: R 247 MET cc_start: 0.7035 (ppp) cc_final: 0.6659 (ppp) REVERT: R 262 MET cc_start: 0.6064 (ppp) cc_final: 0.5793 (ppp) REVERT: R 280 ILE cc_start: 0.7951 (mt) cc_final: 0.7725 (mt) REVERT: R 284 LYS cc_start: 0.7778 (tptp) cc_final: 0.7356 (tptp) REVERT: R 287 LYS cc_start: 0.7751 (tppp) cc_final: 0.7499 (tppp) outliers start: 26 outliers final: 22 residues processed: 239 average time/residue: 0.2610 time to fit residues: 80.6415 Evaluate side-chains 250 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 226 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 267 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 82 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 148 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8617 Z= 0.279 Angle : 0.597 14.367 11673 Z= 0.306 Chirality : 0.042 0.148 1322 Planarity : 0.004 0.047 1475 Dihedral : 4.205 21.439 1147 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.82 % Allowed : 21.56 % Favored : 75.62 % 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: 1.08 (0.26), residues: 1054 helix: 2.37 (0.24), residues: 452 sheet: 0.32 (0.35), residues: 220 loop : -1.11 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 99 HIS 0.003 0.001 HIS A 212 PHE 0.022 0.002 PHE R 9 TYR 0.013 0.001 TYR N 61 ARG 0.010 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2108 Ramachandran restraints generated. 1054 Oldfield, 0 Emsley, 1054 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: A 23 GLU cc_start: 0.7321 (tp30) cc_final: 0.6953 (tp30) REVERT: A 55 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: A 96 ARG cc_start: 0.7229 (ptt180) cc_final: 0.7005 (ptt180) REVERT: A 123 GLU cc_start: 0.6770 (pt0) cc_final: 0.6557 (pt0) REVERT: A 198 ASP cc_start: 0.7211 (t0) cc_final: 0.6878 (m-30) REVERT: A 241 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6345 (mt-10) REVERT: B 256 ARG cc_start: 0.8245 (ptp-110) cc_final: 0.7980 (mtm180) REVERT: N 60 SER cc_start: 0.7789 (m) cc_final: 0.7431 (p) REVERT: N 109 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7411 (m-80) REVERT: R 109 LYS cc_start: 0.7566 (mmmm) cc_final: 0.7220 (mmmm) REVERT: R 112 ASN cc_start: 0.8636 (p0) cc_final: 0.8362 (p0) REVERT: R 207 LYS cc_start: 0.7750 (tmtt) cc_final: 0.7459 (tmtt) REVERT: R 247 MET cc_start: 0.7039 (ppp) cc_final: 0.6507 (ppp) REVERT: R 262 MET cc_start: 0.6090 (ppp) cc_final: 0.5812 (ppp) REVERT: R 284 LYS cc_start: 0.7797 (tptp) cc_final: 0.7371 (tptp) REVERT: R 287 LYS cc_start: 0.7756 (tppp) cc_final: 0.7507 (tppp) outliers start: 26 outliers final: 23 residues processed: 240 average time/residue: 0.2506 time to fit residues: 77.5985 Evaluate side-chains 253 residues out of total 923 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 228 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LYS Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 45 ASP Chi-restraints excluded: chain A residue 55 GLN Chi-restraints excluded: chain A residue 101 GLN Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 154 GLU Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 188 MET Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 247 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 3 VAL Chi-restraints excluded: chain N residue 26 SER Chi-restraints excluded: chain N residue 79 THR Chi-restraints excluded: chain N residue 109 PHE Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 121 LEU Chi-restraints excluded: chain R residue 168 LEU Chi-restraints excluded: chain R residue 201 SER Chi-restraints excluded: chain R residue 267 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 0.0370 chunk 34 optimal weight: 0.5980 chunk 84 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 4 optimal weight: 0.0070 chunk 59 optimal weight: 0.7980 overall best weight: 0.3876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.145344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.127424 restraints weight = 12314.255| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.23 r_work: 0.3548 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8617 Z= 0.171 Angle : 0.562 14.719 11673 Z= 0.286 Chirality : 0.040 0.139 1322 Planarity : 0.004 0.048 1475 Dihedral : 4.000 20.254 1147 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.60 % Allowed : 21.99 % Favored : 75.41 % 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: 1.24 (0.26), residues: 1054 helix: 2.55 (0.24), residues: 449 sheet: 0.33 (0.35), residues: 220 loop : -1.01 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 99 HIS 0.003 0.001 HIS B 54 PHE 0.023 0.001 PHE R 9 TYR 0.008 0.001 TYR N 61 ARG 0.009 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2514.43 seconds wall clock time: 45 minutes 22.10 seconds (2722.10 seconds total)