Starting phenix.real_space_refine on Thu Mar 14 16:29:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/03_2024/8blq_16113.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/03_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_16113/03_2024/8blq_16113.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/03_2024/8blq_16113.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/03_2024/8blq_16113.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8blq_16113/03_2024/8blq_16113.pdb" } 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 Residue "A GLU 57": "OE1" <-> "OE2" Residue "A ARG 59": "NH1" <-> "NH2" Residue "A ARG 63": "NH1" <-> "NH2" Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 84": "NH1" <-> "NH2" Residue "A ARG 98": "NH1" <-> "NH2" Residue "B ARG 18": "NH1" <-> "NH2" Residue "B GLU 97": "OE1" <-> "OE2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 231": "NH1" <-> "NH2" Residue "C ARG 191": "NH1" <-> "NH2" Residue "D ARG 29": "NH1" <-> "NH2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E ARG 87": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.31, per 1000 atoms: 0.58 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 - 3.50 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: 3.42 Conformation dependent library (CDL) restraints added in 1.7 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: 1.17 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: 2.62 Time building geometry restraints manager: 3.78 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: 100.15 - 106.93: 318 106.93 - 113.70: 5217 113.70 - 120.48: 3237 120.48 - 127.26: 3944 127.26 - 134.04: 114 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 2.440 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 106 " model vdw 2.222 2.440 nonbonded pdb=" O HIS C 199 " pdb=" OG SER C 202 " model vdw 2.233 2.440 nonbonded pdb=" OG SER C 194 " pdb=" O LYS C 206 " model vdw 2.234 2.440 nonbonded pdb=" OG SER E 52 " pdb=" OD1 ASN E 55 " model vdw 2.234 2.440 ... (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 ========== 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: 2.560 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: 12.940 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 26.810 Find NCS groups from input model: 0.260 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.490 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.953 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: 0.3064 time to fit residues: 24.4753 Evaluate side-chains 26 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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: 3.9990 chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 20.0000 chunk 31 optimal weight: 30.0000 chunk 61 optimal weight: 10.0000 chunk 48 optimal weight: 20.0000 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 57 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 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 201 GLN ** A 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN A 335 ASN B 34 GLN ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 197 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 283 GLN C 6 GLN ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 36 GLN ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 128 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** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.117 9427 Z= 0.449 Angle : 0.749 11.447 12830 Z= 0.388 Chirality : 0.043 0.133 1438 Planarity : 0.005 0.061 1649 Dihedral : 5.433 89.831 1305 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 28.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.60 % Favored : 91.40 % Rotamer: Outliers : 1.07 % Allowed : 11.11 % Favored : 87.82 % 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: -3.27 (0.23), residues: 1210 helix: -1.06 (0.52), residues: 98 sheet: -2.50 (0.24), residues: 384 loop : -2.17 (0.22), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP A 285 HIS 0.008 0.002 HIS C 190 PHE 0.019 0.003 PHE C 61 TYR 0.019 0.002 TYR B 90 ARG 0.008 0.001 ARG B 334 *********************** 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 36 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 25 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.7603 (tmm) cc_final: 0.6601 (tmm) REVERT: D 102 HIS cc_start: 0.8901 (p-80) cc_final: 0.8594 (p-80) outliers start: 11 outliers final: 7 residues processed: 35 average time/residue: 0.2444 time to fit residues: 12.7975 Evaluate side-chains 28 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 21 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET 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 D residue 94 SER 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: 4.9990 chunk 33 optimal weight: 0.0970 chunk 90 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 87 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- 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 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 201 GLN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN B 83 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 GLN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9427 Z= 0.158 Angle : 0.529 7.813 12830 Z= 0.269 Chirality : 0.042 0.143 1438 Planarity : 0.004 0.037 1649 Dihedral : 4.838 85.593 1305 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.07 % Allowed : 13.35 % Favored : 85.58 % 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: -2.80 (0.23), residues: 1210 helix: -0.54 (0.55), residues: 98 sheet: -2.23 (0.24), residues: 398 loop : -1.83 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 160 HIS 0.002 0.001 HIS B 38 PHE 0.013 0.001 PHE A 29 TYR 0.012 0.001 TYR A 307 ARG 0.003 0.000 ARG E 106 *********************** 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 34 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 23 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.7574 (tmm) cc_final: 0.6656 (tmm) REVERT: D 102 HIS cc_start: 0.8936 (p-80) cc_final: 0.8622 (p-80) REVERT: E 48 MET cc_start: 0.8762 (mmm) cc_final: 0.8456 (mmm) outliers start: 11 outliers final: 6 residues processed: 33 average time/residue: 0.2465 time to fit residues: 12.4523 Evaluate side-chains 25 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain D residue 91 HIS Chi-restraints excluded: chain D residue 94 SER Chi-restraints excluded: chain E residue 193 VAL 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: 0.2980 chunk 56 optimal weight: 10.0000 chunk 12 optimal weight: 0.0770 chunk 52 optimal weight: 30.0000 chunk 73 optimal weight: 6.9990 chunk 109 optimal weight: 0.9980 chunk 115 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 103 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 1.6742 ------------------------------------------------------------------------------- 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 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9427 Z= 0.186 Angle : 0.522 8.241 12830 Z= 0.264 Chirality : 0.041 0.142 1438 Planarity : 0.004 0.038 1649 Dihedral : 4.788 83.862 1305 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.27 % Favored : 92.73 % Rotamer: Outliers : 1.27 % Allowed : 14.42 % Favored : 84.31 % 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: -2.45 (0.24), residues: 1210 helix: -0.25 (0.57), residues: 92 sheet: -1.96 (0.25), residues: 392 loop : -1.61 (0.23), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 50 HIS 0.003 0.001 HIS B 38 PHE 0.013 0.001 PHE A 29 TYR 0.013 0.001 TYR A 307 ARG 0.005 0.000 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 32 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 19 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.7483 (tmm) cc_final: 0.6852 (tmm) REVERT: D 61 MET cc_start: 0.8672 (pmm) cc_final: 0.8472 (pmm) REVERT: D 102 HIS cc_start: 0.9045 (p-80) cc_final: 0.8703 (p-80) REVERT: E 48 MET cc_start: 0.8940 (mmm) cc_final: 0.8194 (mmm) outliers start: 13 outliers final: 7 residues processed: 30 average time/residue: 0.2168 time to fit residues: 10.6024 Evaluate side-chains 25 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 18 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 174 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 86 optimal weight: 0.6980 chunk 47 optimal weight: 0.0070 chunk 98 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 59 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 29 optimal weight: 30.0000 overall best weight: 0.7198 ------------------------------------------------------------------------------- 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 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9427 Z= 0.126 Angle : 0.492 6.615 12830 Z= 0.247 Chirality : 0.041 0.134 1438 Planarity : 0.004 0.041 1649 Dihedral : 4.566 80.391 1305 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.46 % Allowed : 15.01 % Favored : 83.53 % 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: -2.13 (0.24), residues: 1210 helix: 0.05 (0.57), residues: 93 sheet: -1.77 (0.24), residues: 406 loop : -1.37 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.002 0.001 HIS D 120 PHE 0.011 0.001 PHE A 29 TYR 0.012 0.001 TYR A 307 ARG 0.003 0.000 ARG E 106 *********************** 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 35 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 20 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 61 MET cc_start: 0.8748 (pmm) cc_final: 0.8321 (pmm) REVERT: D 84 MET cc_start: 0.9309 (mtm) cc_final: 0.9031 (mtm) REVERT: D 102 HIS cc_start: 0.9064 (p-80) cc_final: 0.8744 (p-80) REVERT: E 70 MET cc_start: 0.7174 (tpt) cc_final: 0.6620 (ttm) outliers start: 15 outliers final: 10 residues processed: 32 average time/residue: 0.1969 time to fit residues: 10.1978 Evaluate side-chains 29 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 19 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 81 MET Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 328 ASN 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 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: 6.9990 chunk 104 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 20.0000 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 65 GLN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 9427 Z= 0.271 Angle : 0.558 8.976 12830 Z= 0.284 Chirality : 0.041 0.147 1438 Planarity : 0.004 0.041 1649 Dihedral : 4.839 78.868 1305 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer: Outliers : 1.95 % Allowed : 15.01 % Favored : 83.04 % 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: -2.00 (0.24), residues: 1210 helix: -0.19 (0.55), residues: 98 sheet: -1.64 (0.25), residues: 405 loop : -1.26 (0.24), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 50 HIS 0.004 0.001 HIS B 38 PHE 0.012 0.002 PHE B 75 TYR 0.013 0.001 TYR A 307 ARG 0.008 0.001 ARG B 334 *********************** 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 39 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 19 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.7510 (tmm) cc_final: 0.6850 (tmm) REVERT: D 61 MET cc_start: 0.8968 (pmm) cc_final: 0.8530 (pmm) REVERT: D 84 MET cc_start: 0.9371 (mtm) cc_final: 0.9075 (mtm) REVERT: E 48 MET cc_start: 0.8871 (mmm) cc_final: 0.8634 (mmm) outliers start: 20 outliers final: 11 residues processed: 35 average time/residue: 0.2162 time to fit residues: 12.0105 Evaluate side-chains 29 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 18 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 174 MET Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 11 LEU 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 30 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: 0.4980 chunk 13 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 84 optimal weight: 10.0000 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 115 optimal weight: 0.3980 chunk 72 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN B 247 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.4272 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= 0.137 Angle : 0.502 7.130 12830 Z= 0.252 Chirality : 0.042 0.190 1438 Planarity : 0.004 0.044 1649 Dihedral : 4.545 73.224 1305 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 1.27 % Allowed : 16.08 % 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: -1.83 (0.24), residues: 1210 helix: 0.14 (0.56), residues: 94 sheet: -1.54 (0.25), residues: 412 loop : -1.15 (0.24), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 160 HIS 0.003 0.001 HIS D 120 PHE 0.009 0.001 PHE B 241 TYR 0.013 0.001 TYR A 307 ARG 0.003 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 31 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 18 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.7356 (tmm) cc_final: 0.6960 (tmm) REVERT: D 61 MET cc_start: 0.8914 (pmm) cc_final: 0.8458 (pmm) REVERT: E 48 MET cc_start: 0.8853 (mmm) cc_final: 0.8642 (mmm) outliers start: 13 outliers final: 9 residues processed: 30 average time/residue: 0.2025 time to fit residues: 10.0588 Evaluate side-chains 27 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 18 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 174 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 C residue 183 THR Chi-restraints excluded: chain D residue 91 HIS 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: 0.6980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 10.0000 chunk 90 optimal weight: 0.0020 chunk 105 optimal weight: 7.9990 overall best weight: 2.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 9427 Z= 0.212 Angle : 0.529 9.178 12830 Z= 0.267 Chirality : 0.041 0.157 1438 Planarity : 0.004 0.043 1649 Dihedral : 4.646 72.116 1305 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 1.17 % Allowed : 16.18 % 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: -1.74 (0.25), residues: 1210 helix: -0.04 (0.54), residues: 100 sheet: -1.50 (0.24), residues: 445 loop : -0.99 (0.26), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 50 HIS 0.003 0.001 HIS B 38 PHE 0.011 0.001 PHE B 75 TYR 0.015 0.001 TYR A 307 ARG 0.005 0.000 ARG B 334 *********************** 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 30 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 18 time to evaluate : 1.060 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.7378 (tmm) cc_final: 0.6898 (tmm) REVERT: D 61 MET cc_start: 0.8992 (pmm) cc_final: 0.8490 (pmm) REVERT: D 84 MET cc_start: 0.9327 (mtm) cc_final: 0.9079 (mtm) REVERT: E 48 MET cc_start: 0.8836 (mmm) cc_final: 0.8568 (mmm) outliers start: 12 outliers final: 11 residues processed: 28 average time/residue: 0.1967 time to fit residues: 9.2559 Evaluate side-chains 29 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 18 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 174 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 C residue 183 THR Chi-restraints excluded: chain D residue 91 HIS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 33 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.5259 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= 0.229 Angle : 0.550 7.248 12830 Z= 0.280 Chirality : 0.041 0.175 1438 Planarity : 0.004 0.043 1649 Dihedral : 4.847 66.869 1305 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.36 % Allowed : 16.28 % Favored : 82.36 % 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: -1.70 (0.25), residues: 1210 helix: -0.04 (0.54), residues: 99 sheet: -1.44 (0.24), residues: 457 loop : -0.96 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 53 HIS 0.004 0.001 HIS B 38 PHE 0.012 0.002 PHE B 216 TYR 0.015 0.001 TYR A 307 ARG 0.006 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 33 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 19 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 37 MET cc_start: 0.7486 (tmm) cc_final: 0.6932 (tmm) REVERT: D 51 MET cc_start: 0.8420 (tpp) cc_final: 0.8146 (tpp) REVERT: D 61 MET cc_start: 0.9038 (pmm) cc_final: 0.8485 (pmm) REVERT: E 48 MET cc_start: 0.8833 (mmm) cc_final: 0.8576 (mmm) outliers start: 14 outliers final: 11 residues processed: 30 average time/residue: 0.1895 time to fit residues: 9.4064 Evaluate side-chains 29 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 18 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ILE 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 C residue 183 THR Chi-restraints excluded: chain D residue 91 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 119 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 29 optimal weight: 20.0000 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 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 GLN ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.6133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 9427 Z= 0.419 Angle : 0.714 10.395 12830 Z= 0.361 Chirality : 0.043 0.152 1438 Planarity : 0.005 0.040 1649 Dihedral : 5.605 65.221 1305 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 34.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.26 % Favored : 90.74 % Rotamer: Outliers : 1.17 % Allowed : 16.47 % Favored : 82.36 % 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: -2.01 (0.24), residues: 1210 helix: -0.42 (0.54), residues: 98 sheet: -1.63 (0.24), residues: 451 loop : -1.17 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 113 HIS 0.007 0.002 HIS B 38 PHE 0.019 0.003 PHE E 108 TYR 0.017 0.002 TYR C 179 ARG 0.011 0.001 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 31 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 19 time to evaluate : 1.165 Fit side-chains revert: symmetry clash REVERT: B 37 MET cc_start: 0.7734 (tmm) cc_final: 0.6923 (tmm) REVERT: D 51 MET cc_start: 0.8639 (tpp) cc_final: 0.8349 (tpp) REVERT: D 61 MET cc_start: 0.9147 (pmm) cc_final: 0.8539 (pmm) REVERT: E 48 MET cc_start: 0.8842 (mmm) cc_final: 0.8560 (mmm) outliers start: 12 outliers final: 10 residues processed: 29 average time/residue: 0.1955 time to fit residues: 9.5634 Evaluate side-chains 28 residues out of total 1026 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 18 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 MET Chi-restraints excluded: chain A residue 159 ASN 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 D residue 91 HIS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 GLN ** C 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.032765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.025454 restraints weight = 173062.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.026070 restraints weight = 104567.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.026485 restraints weight = 73039.971| |-----------------------------------------------------------------------------| r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9427 Z= 0.211 Angle : 0.562 8.293 12830 Z= 0.284 Chirality : 0.042 0.164 1438 Planarity : 0.004 0.038 1649 Dihedral : 5.057 55.815 1305 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 24.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 0.97 % Allowed : 17.15 % Favored : 81.87 % 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: -1.76 (0.25), residues: 1210 helix: -0.25 (0.53), residues: 99 sheet: -1.50 (0.24), residues: 432 loop : -1.00 (0.25), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 285 HIS 0.004 0.001 HIS B 321 PHE 0.012 0.001 PHE B 75 TYR 0.013 0.001 TYR A 307 ARG 0.006 0.001 ARG B 334 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1734.35 seconds wall clock time: 32 minutes 52.56 seconds (1972.56 seconds total)