Starting phenix.real_space_refine on Fri Nov 15 17:32:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/11_2024/8blq_16113.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/11_2024/8blq_16113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/11_2024/8blq_16113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/11_2024/8blq_16113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/11_2024/8blq_16113.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/11_2024/8blq_16113.cif" } resolution = 3.97 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 38 5.16 5 C 5787 2.51 5 N 1550 2.21 5 O 1835 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9210 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2597 Classifications: {'peptide': 343} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 16, 'TRANS': 322} Chain: "B" Number of atoms: 2514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2514 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PCIS': 5, 'PTRANS': 11, 'TRANS': 317} Chain: "C" Number of atoms: 1584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1584 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 194} Chain: "D" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "E" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1671 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 210} Time building chain proxies: 5.87, per 1000 atoms: 0.64 Number of scatterers: 9210 At special positions: 0 Unit cell: (167.881, 118.261, 87.662, 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 38 16.00 O 1835 8.00 N 1550 7.00 C 5787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 219 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 92 " distance=2.03 Simple disulfide: pdb=" SG CYS B 257 " - pdb=" SG CYS B 317 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2214 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 30 sheets defined 11.8% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.628A pdb=" N SER A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 156 Processing helix chain 'A' and resid 210 through 214 Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'B' and resid 197 through 201 removed outlier: 3.560A pdb=" N ILE B 201 " --> pdb=" O PRO B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.680A pdb=" N LYS B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 82 Processing helix chain 'C' and resid 123 through 129 Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.576A pdb=" N HIS C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 39 removed outlier: 4.253A pdb=" N LEU D 28 " --> pdb=" O PRO D 24 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG D 29 " --> pdb=" O SER D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 50 removed outlier: 4.160A pdb=" N GLY D 49 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N SER D 50 " --> pdb=" O CYS D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 70 Processing helix chain 'D' and resid 78 through 89 Processing helix chain 'D' and resid 94 through 98 removed outlier: 3.713A pdb=" N GLN D 97 " --> pdb=" O SER D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 105 removed outlier: 3.622A pdb=" N VAL D 103 " --> pdb=" O SER D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 127 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 194 through 198 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.501A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.782A pdb=" N ILE A 37 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 102 removed outlier: 3.777A pdb=" N LYS A 100 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 127 through 131 removed outlier: 3.559A pdb=" N GLN A 127 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 182 removed outlier: 5.352A pdb=" N TRP A 171 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG A 162 " --> pdb=" O TRP A 171 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 173 " --> pdb=" O TRP A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 181 through 182 removed outlier: 5.352A pdb=" N TRP A 171 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ARG A 162 " --> pdb=" O TRP A 171 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY A 173 " --> pdb=" O TRP A 160 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ARG A 221 " --> pdb=" O ASP A 230 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.739A pdb=" N SER A 192 " --> pdb=" O GLU A 205 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 253 through 255 Processing sheet with id=AA9, first strand: chain 'A' and resid 267 through 268 removed outlier: 6.537A pdb=" N SER A 311 " --> pdb=" O ALA A 299 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ALA A 299 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N VAL A 313 " --> pdb=" O PHE A 297 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 282 through 285 Processing sheet with id=AB2, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.563A pdb=" N SER B 22 " --> pdb=" O SER B 7 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 76 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER B 69 " --> pdb=" O THR B 76 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'B' and resid 30 through 31 Processing sheet with id=AB5, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.586A pdb=" N LEU B 51 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TRP B 39 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET B 37 " --> pdb=" O TYR B 53 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 57 through 58 removed outlier: 3.586A pdb=" N LEU B 51 " --> pdb=" O TRP B 39 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N TRP B 39 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N TYR B 53 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET B 37 " --> pdb=" O TYR B 53 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN B 94 " --> pdb=" O THR B 101 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR B 101 " --> pdb=" O GLN B 94 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 140 through 142 Processing sheet with id=AB8, first strand: chain 'B' and resid 171 through 172 removed outlier: 6.805A pdb=" N TRP B 153 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 238 through 240 removed outlier: 4.191A pdb=" N SER B 254 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 304 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N VAL B 256 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 302 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 258 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER B 300 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N ASN B 260 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LEU B 298 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER B 285 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 267 through 269 Processing sheet with id=AC2, first strand: chain 'B' and resid 272 through 273 removed outlier: 4.439A pdb=" N TYR B 315 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N PHE B 332 " --> pdb=" O TYR B 315 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS B 317 " --> pdb=" O LYS B 330 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LYS B 330 " --> pdb=" O CYS B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.586A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN C 88 " --> pdb=" O HIS C 33 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 9 through 12 removed outlier: 6.586A pdb=" N VAL C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL C 89 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL C 98 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 18 through 22 removed outlier: 4.096A pdb=" N ALA C 70 " --> pdb=" O CYS C 22 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 116 through 120 removed outlier: 3.548A pdb=" N VAL C 135 " --> pdb=" O PHE C 120 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA C 132 " --> pdb=" O LEU C 182 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N TYR C 174 " --> pdb=" O ASP C 140 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 155 through 156 removed outlier: 3.698A pdb=" N CYS C 195 " --> pdb=" O LYS C 206 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS C 206 " --> pdb=" O CYS C 195 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AC9, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AD1, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.766A pdb=" N VAL E 118 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA E 92 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL E 37 " --> pdb=" O TYR E 95 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 129 through 132 removed outlier: 3.583A pdb=" N PHE E 131 " --> pdb=" O LEU E 150 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER E 189 " --> pdb=" O CYS E 149 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP E 153 " --> pdb=" O TYR E 185 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TYR E 185 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 159 through 163 removed outlier: 3.525A pdb=" N VAL E 207 " --> pdb=" O VAL E 216 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 216 " --> pdb=" O VAL E 207 " (cutoff:3.500A) 271 hydrogen bonds defined for protein. 609 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: 2.81 Time building geometry restraints manager: 2.59 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: 2973 1.34 - 1.46: 2242 1.46 - 1.58: 4161 1.58 - 1.70: 0 1.70 - 1.81: 51 Bond restraints: 9427 Sorted by residual: bond pdb=" N ILE C 26 " pdb=" CA ILE C 26 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.25e-02 6.40e+03 6.19e+00 bond pdb=" N ASN C 25 " pdb=" CA ASN C 25 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.13e+00 bond pdb=" N ILE C 27 " pdb=" CA ILE C 27 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.28e-02 6.10e+03 5.46e+00 bond pdb=" C LYS E 210 " pdb=" N PRO E 211 " ideal model delta sigma weight residual 1.335 1.351 -0.016 1.30e-02 5.92e+03 1.51e+00 bond pdb=" CG PRO B 264 " pdb=" CD PRO B 264 " ideal model delta sigma weight residual 1.512 1.483 0.029 2.70e-02 1.37e+03 1.13e+00 ... (remaining 9422 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 12465 1.40 - 2.80: 320 2.80 - 4.20: 37 4.20 - 5.61: 2 5.61 - 7.01: 6 Bond angle restraints: 12830 Sorted by residual: angle pdb=" N ILE C 27 " pdb=" CA ILE C 27 " pdb=" C ILE C 27 " ideal model delta sigma weight residual 113.16 106.50 6.66 1.49e+00 4.50e-01 2.00e+01 angle pdb=" C ILE B 147 " pdb=" N ASP B 148 " pdb=" CA ASP B 148 " ideal model delta sigma weight residual 121.54 128.55 -7.01 1.91e+00 2.74e-01 1.35e+01 angle pdb=" N ILE B 147 " pdb=" CA ILE B 147 " pdb=" C ILE B 147 " ideal model delta sigma weight residual 111.62 108.83 2.79 7.90e-01 1.60e+00 1.25e+01 angle pdb=" C GLY D 74 " pdb=" N CYS D 75 " pdb=" CA CYS D 75 " ideal model delta sigma weight residual 121.54 127.75 -6.21 1.91e+00 2.74e-01 1.06e+01 angle pdb=" N THR C 69 " pdb=" CA THR C 69 " pdb=" C THR C 69 " ideal model delta sigma weight residual 107.93 111.74 -3.81 1.65e+00 3.67e-01 5.32e+00 ... (remaining 12825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 5162 17.84 - 35.68: 367 35.68 - 53.52: 57 53.52 - 71.37: 9 71.37 - 89.21: 3 Dihedral angle restraints: 5598 sinusoidal: 2120 harmonic: 3478 Sorted by residual: dihedral pdb=" CB CYS A 22 " pdb=" SG CYS A 22 " pdb=" SG CYS A 96 " pdb=" CB CYS A 96 " ideal model delta sinusoidal sigma weight residual 93.00 144.69 -51.69 1 1.00e+01 1.00e-02 3.65e+01 dihedral pdb=" CB CYS C 22 " pdb=" SG CYS C 22 " pdb=" SG CYS C 87 " pdb=" CB CYS C 87 " ideal model delta sinusoidal sigma weight residual 93.00 46.53 46.47 1 1.00e+01 1.00e-02 2.99e+01 dihedral pdb=" CA SER B 71 " pdb=" C SER B 71 " pdb=" N ARG B 72 " pdb=" CA ARG B 72 " ideal model delta harmonic sigma weight residual 180.00 162.47 17.53 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 5595 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1016 0.037 - 0.074: 287 0.074 - 0.111: 118 0.111 - 0.148: 15 0.148 - 0.185: 2 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA ILE C 27 " pdb=" N ILE C 27 " pdb=" C ILE C 27 " pdb=" CB ILE C 27 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA ILE C 26 " pdb=" N ILE C 26 " pdb=" C ILE C 26 " pdb=" CB ILE C 26 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" CB ILE B 137 " pdb=" CA ILE B 137 " pdb=" CG1 ILE B 137 " pdb=" CG2 ILE B 137 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.27e-01 ... (remaining 1435 not shown) Planarity restraints: 1649 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 279 " 0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 280 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 280 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 280 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 24 " -0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C GLY C 24 " 0.024 2.00e-02 2.50e+03 pdb=" O GLY C 24 " -0.009 2.00e-02 2.50e+03 pdb=" N ASN C 25 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 183 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.75e+00 pdb=" N PRO C 184 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 184 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 184 " 0.018 5.00e-02 4.00e+02 ... (remaining 1646 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 794 2.74 - 3.28: 9273 3.28 - 3.82: 15357 3.82 - 4.36: 17650 4.36 - 4.90: 30315 Nonbonded interactions: 73389 Sorted by model distance: nonbonded pdb=" O GLN C 186 " pdb=" OH TYR C 193 " model vdw 2.201 3.040 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 106 " model vdw 2.222 3.040 nonbonded pdb=" O HIS C 199 " pdb=" OG SER C 202 " model vdw 2.233 3.040 nonbonded pdb=" OG SER C 194 " pdb=" O LYS C 206 " model vdw 2.234 3.040 nonbonded pdb=" OG SER E 52 " pdb=" OD1 ASN E 55 " model vdw 2.234 3.040 ... (remaining 73384 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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 group one per residue 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: 4.310 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.590 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 0.002 0.034 9427 Z= 0.146 Angle : 0.551 7.007 12830 Z= 0.320 Chirality : 0.041 0.185 1438 Planarity : 0.004 0.037 1649 Dihedral : 12.200 89.206 3363 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % 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: -3.81 (0.22), residues: 1210 helix: -1.23 (0.49), residues: 91 sheet: -2.75 (0.22), residues: 412 loop : -2.61 (0.21), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.002 0.000 HIS A 295 PHE 0.009 0.001 PHE B 189 TYR 0.006 0.001 TYR A 218 ARG 0.001 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 61 average time/residue: 0.3283 time to fit residues: 26.3473 Evaluate side-chains 26 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 30.0000 chunk 31 optimal weight: 30.0000 chunk 61 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 335 ASN B 6 GLN B 17 GLN B 41 GLN B 83 GLN ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 6 GLN C 36 GLN C 128 GLN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 3 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.118 9427 Z= 0.458 Angle : 0.775 11.032 12830 Z= 0.400 Chirality : 0.044 0.152 1438 Planarity : 0.005 0.061 1649 Dihedral : 5.465 89.758 1305 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 1.56 % Allowed : 10.14 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % 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: -3.16 (0.23), residues: 1210 helix: -1.03 (0.52), residues: 93 sheet: -2.58 (0.24), residues: 402 loop : -1.94 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP A 285 HIS 0.009 0.002 HIS C 190 PHE 0.022 0.003 PHE B 75 TYR 0.017 0.002 TYR C 193 ARG 0.008 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 28 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.4319 (OUTLIER) cc_final: 0.3578 (mm-30) REVERT: D 84 MET cc_start: 0.9390 (mtm) cc_final: 0.8958 (mtm) outliers start: 16 outliers final: 7 residues processed: 42 average time/residue: 0.2348 time to fit residues: 14.7550 Evaluate side-chains 28 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain C residue 26 ILE Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain E residue 193 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 HIS B 260 ASN B 261 ASN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN D 40 GLN E 6 GLN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9427 Z= 0.199 Angle : 0.558 8.746 12830 Z= 0.286 Chirality : 0.043 0.169 1438 Planarity : 0.004 0.037 1649 Dihedral : 5.027 86.514 1305 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 0.97 % Allowed : 12.87 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % 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: -2.73 (0.23), residues: 1210 helix: -0.76 (0.53), residues: 99 sheet: -2.18 (0.24), residues: 379 loop : -1.76 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 160 HIS 0.003 0.001 HIS B 38 PHE 0.028 0.002 PHE B 239 TYR 0.011 0.001 TYR A 307 ARG 0.004 0.001 ARG A 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 23 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.7557 (tmm) cc_final: 0.6496 (tmm) REVERT: D 61 MET cc_start: 0.8903 (pmm) cc_final: 0.8514 (pmm) REVERT: D 84 MET cc_start: 0.9301 (mtm) cc_final: 0.9101 (mtm) outliers start: 10 outliers final: 6 residues processed: 32 average time/residue: 0.2316 time to fit residues: 11.4249 Evaluate side-chains 26 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain E residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 73 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 115 optimal weight: 30.0000 chunk 57 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 6.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 3 GLN ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN A 286 ASN A 323 GLN ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9427 Z= 0.228 Angle : 0.560 9.129 12830 Z= 0.284 Chirality : 0.042 0.133 1438 Planarity : 0.004 0.039 1649 Dihedral : 5.012 83.131 1305 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.66 % Allowed : 13.55 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % 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: -2.33 (0.24), residues: 1210 helix: -0.51 (0.54), residues: 99 sheet: -1.93 (0.25), residues: 386 loop : -1.46 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 50 HIS 0.004 0.001 HIS D 102 PHE 0.013 0.002 PHE B 239 TYR 0.008 0.001 TYR B 90 ARG 0.005 0.001 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 20 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.4301 (OUTLIER) cc_final: 0.3471 (mm-30) REVERT: B 37 MET cc_start: 0.7451 (tmm) cc_final: 0.6694 (tmm) REVERT: D 61 MET cc_start: 0.9069 (pmm) cc_final: 0.8467 (pmm) REVERT: E 48 MET cc_start: 0.8818 (mmm) cc_final: 0.8525 (mmm) outliers start: 17 outliers final: 9 residues processed: 36 average time/residue: 0.2195 time to fit residues: 12.0729 Evaluate side-chains 28 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 18 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 193 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 47 optimal weight: 6.9990 chunk 98 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 59 optimal weight: 8.9990 chunk 104 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.094 9427 Z= 0.441 Angle : 0.757 12.478 12830 Z= 0.383 Chirality : 0.044 0.197 1438 Planarity : 0.005 0.047 1649 Dihedral : 5.946 78.546 1305 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 28.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 2.92 % Allowed : 14.42 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % 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: -2.47 (0.24), residues: 1210 helix: -1.03 (0.51), residues: 99 sheet: -1.96 (0.25), residues: 394 loop : -1.51 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 113 HIS 0.007 0.002 HIS B 38 PHE 0.020 0.003 PHE B 216 TYR 0.018 0.002 TYR C 179 ARG 0.012 0.001 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 18 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 GLU cc_start: 0.8494 (tp30) cc_final: 0.8207 (tm-30) REVERT: D 61 MET cc_start: 0.9266 (pmm) cc_final: 0.8545 (pmm) REVERT: E 48 MET cc_start: 0.8742 (mmm) cc_final: 0.8371 (mmm) outliers start: 30 outliers final: 18 residues processed: 45 average time/residue: 0.1895 time to fit residues: 13.7185 Evaluate side-chains 36 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 18 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain B residue 275 ASN Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 220 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 68 optimal weight: 8.9990 chunk 28 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 53 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 38 optimal weight: 0.3980 chunk 60 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.5058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9427 Z= 0.163 Angle : 0.564 7.743 12830 Z= 0.286 Chirality : 0.043 0.150 1438 Planarity : 0.004 0.038 1649 Dihedral : 5.047 68.284 1305 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 1.46 % Allowed : 16.37 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % 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: -2.10 (0.24), residues: 1210 helix: -0.65 (0.52), residues: 100 sheet: -1.68 (0.25), residues: 386 loop : -1.31 (0.24), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 47 HIS 0.006 0.001 HIS B 38 PHE 0.008 0.001 PHE A 108 TYR 0.009 0.001 TYR B 212 ARG 0.003 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 20 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.4307 (OUTLIER) cc_final: 0.3361 (mm-30) REVERT: A 101 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5269 (tm-30) REVERT: A 343 GLU cc_start: 0.8179 (tp30) cc_final: 0.7838 (tm-30) REVERT: D 61 MET cc_start: 0.9154 (pmm) cc_final: 0.8482 (pmm) REVERT: E 48 MET cc_start: 0.8825 (mmm) cc_final: 0.8551 (mmm) outliers start: 15 outliers final: 12 residues processed: 34 average time/residue: 0.2040 time to fit residues: 11.3407 Evaluate side-chains 33 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 19 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 220 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 9.9990 chunk 84 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 115 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 53 optimal weight: 0.0370 overall best weight: 3.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9427 Z= 0.291 Angle : 0.598 8.700 12830 Z= 0.305 Chirality : 0.042 0.131 1438 Planarity : 0.004 0.038 1649 Dihedral : 5.270 69.294 1305 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 18.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 2.34 % Allowed : 16.18 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % 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: -2.03 (0.24), residues: 1210 helix: -0.65 (0.53), residues: 99 sheet: -1.60 (0.26), residues: 388 loop : -1.27 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 47 HIS 0.006 0.001 HIS B 38 PHE 0.012 0.002 PHE B 216 TYR 0.010 0.001 TYR B 90 ARG 0.004 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 19 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 TRP cc_start: 0.6410 (OUTLIER) cc_final: 0.5967 (t60) REVERT: A 101 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5421 (tm-30) REVERT: A 343 GLU cc_start: 0.8464 (tp30) cc_final: 0.8189 (tm-30) REVERT: D 61 MET cc_start: 0.9224 (pmm) cc_final: 0.8429 (pmm) REVERT: E 48 MET cc_start: 0.8774 (mmm) cc_final: 0.8400 (mmm) outliers start: 24 outliers final: 17 residues processed: 41 average time/residue: 0.1882 time to fit residues: 12.5714 Evaluate side-chains 37 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 18 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 169 THR Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 220 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 57 optimal weight: 8.9990 chunk 10 optimal weight: 0.4980 chunk 90 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9427 Z= 0.151 Angle : 0.562 9.776 12830 Z= 0.282 Chirality : 0.042 0.145 1438 Planarity : 0.004 0.039 1649 Dihedral : 4.861 61.908 1305 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.66 % Allowed : 16.86 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % 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: -1.98 (0.24), residues: 1210 helix: -0.54 (0.54), residues: 99 sheet: -1.47 (0.25), residues: 403 loop : -1.30 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 47 HIS 0.002 0.001 HIS D 120 PHE 0.012 0.001 PHE B 262 TYR 0.009 0.001 TYR B 40 ARG 0.003 0.000 ARG E 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 18 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 47 TRP cc_start: 0.6129 (OUTLIER) cc_final: 0.5853 (t60) REVERT: A 74 GLU cc_start: 0.4344 (OUTLIER) cc_final: 0.3437 (mm-30) REVERT: A 101 GLU cc_start: 0.5735 (OUTLIER) cc_final: 0.5103 (tm-30) REVERT: A 343 GLU cc_start: 0.8275 (tp30) cc_final: 0.7968 (tm-30) REVERT: D 61 MET cc_start: 0.9142 (pmm) cc_final: 0.8377 (pmm) REVERT: E 48 MET cc_start: 0.8840 (mmm) cc_final: 0.8584 (mmm) outliers start: 17 outliers final: 10 residues processed: 33 average time/residue: 0.1971 time to fit residues: 10.5132 Evaluate side-chains 31 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 18 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 47 TRP Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 220 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 69 optimal weight: 0.0570 overall best weight: 1.5502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7548 moved from start: 0.5517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9427 Z= 0.178 Angle : 0.558 8.558 12830 Z= 0.281 Chirality : 0.042 0.146 1438 Planarity : 0.004 0.039 1649 Dihedral : 4.778 59.940 1305 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.56 % Allowed : 16.76 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % 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: -1.86 (0.24), residues: 1210 helix: -0.52 (0.53), residues: 99 sheet: -1.35 (0.26), residues: 399 loop : -1.24 (0.24), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 53 HIS 0.002 0.001 HIS D 120 PHE 0.009 0.001 PHE B 262 TYR 0.008 0.001 TYR B 40 ARG 0.003 0.000 ARG B 334 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 18 time to evaluate : 1.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5146 (tm-30) REVERT: A 229 MET cc_start: 0.8171 (mtm) cc_final: 0.7529 (mtm) REVERT: A 343 GLU cc_start: 0.8333 (tp30) cc_final: 0.8050 (tm-30) REVERT: D 61 MET cc_start: 0.9165 (pmm) cc_final: 0.8391 (pmm) REVERT: E 48 MET cc_start: 0.8809 (mmm) cc_final: 0.8505 (mmm) outliers start: 16 outliers final: 11 residues processed: 32 average time/residue: 0.1996 time to fit residues: 10.6047 Evaluate side-chains 30 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 18 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain C residue 183 THR Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 9.9990 chunk 79 optimal weight: 9.9990 chunk 119 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.5835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9427 Z= 0.230 Angle : 0.583 8.526 12830 Z= 0.295 Chirality : 0.042 0.140 1438 Planarity : 0.004 0.041 1649 Dihedral : 4.963 57.491 1305 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 1.56 % Allowed : 17.06 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.24), residues: 1210 helix: -0.56 (0.53), residues: 99 sheet: -1.29 (0.26), residues: 403 loop : -1.31 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 47 HIS 0.003 0.001 HIS B 38 PHE 0.010 0.002 PHE B 75 TYR 0.009 0.001 TYR B 90 ARG 0.004 0.000 ARG B 334 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2420 Ramachandran restraints generated. 1210 Oldfield, 0 Emsley, 1210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 19 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 GLU cc_start: 0.5836 (OUTLIER) cc_final: 0.5186 (tm-30) REVERT: A 229 MET cc_start: 0.8144 (mtm) cc_final: 0.7556 (mtm) REVERT: A 343 GLU cc_start: 0.8532 (tp30) cc_final: 0.8272 (tm-30) REVERT: D 61 MET cc_start: 0.9194 (pmm) cc_final: 0.8335 (pmm) REVERT: E 48 MET cc_start: 0.8754 (mmm) cc_final: 0.8386 (mmm) outliers start: 16 outliers final: 12 residues processed: 33 average time/residue: 0.1758 time to fit residues: 9.8525 Evaluate side-chains 32 residues out of total 1026 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 19 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 122 MET Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain E residue 30 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 172 VAL Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 220 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 39 optimal weight: 0.0870 chunk 97 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.032367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.024904 restraints weight = 173228.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.025537 restraints weight = 103453.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.025986 restraints weight = 71293.407| |-----------------------------------------------------------------------------| r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9427 Z= 0.175 Angle : 0.551 8.846 12830 Z= 0.279 Chirality : 0.042 0.151 1438 Planarity : 0.004 0.041 1649 Dihedral : 4.715 49.869 1305 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.56 % Allowed : 16.96 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % Cis-general : 0.09 % 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: -1.83 (0.24), residues: 1210 helix: -0.49 (0.53), residues: 99 sheet: -1.34 (0.25), residues: 422 loop : -1.18 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 47 HIS 0.003 0.001 HIS B 38 PHE 0.009 0.001 PHE B 75 TYR 0.007 0.001 TYR B 315 ARG 0.003 0.000 ARG B 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1775.81 seconds wall clock time: 34 minutes 10.55 seconds (2050.55 seconds total)