Starting phenix.real_space_refine on Tue Jun 25 20:42:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/06_2024/8ykw_39374_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/06_2024/8ykw_39374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/06_2024/8ykw_39374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/06_2024/8ykw_39374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/06_2024/8ykw_39374_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ykw_39374/06_2024/8ykw_39374_neut_updated.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.081 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 55 5.16 5 C 5574 2.51 5 N 1481 2.21 5 O 1608 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 275": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A GLU 298": "OE1" <-> "OE2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "R GLU 33": "OE1" <-> "OE2" Residue "R PHE 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 153": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 8718 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1713 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1713 Classifications: {'peptide': 213} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 210} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2560 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 19 Chain: "E" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1719 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 55 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 6, 'TYR:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "G" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 440 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "R" Number of atoms: 2278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2278 Classifications: {'peptide': 284} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 12, 'TRANS': 271} Chain breaks: 3 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SIN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.60 Number of scatterers: 8718 At special positions: 0 Unit cell: (86.1, 119.72, 135.3, 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 55 16.00 O 1608 8.00 N 1481 7.00 C 5574 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 11 " - pdb=" SG CYS R 268 " distance=2.30 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2108 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 13 sheets defined 35.4% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.746A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 212 through 215 Processing helix chain 'A' and resid 242 through 254 Processing helix chain 'A' and resid 257 through 259 No H-bonds generated for 'chain 'A' and resid 257 through 259' Processing helix chain 'A' and resid 271 through 279 removed outlier: 3.951A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.069A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 351 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 30 through 34 Processing helix chain 'E' and resid 29 through 31 No H-bonds generated for 'chain 'E' and resid 29 through 31' Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' Processing helix chain 'R' and resid 11 through 23 Processing helix chain 'R' and resid 25 through 48 Processing helix chain 'R' and resid 57 through 85 removed outlier: 3.728A pdb=" N THR R 75 " --> pdb=" O ALA R 71 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LEU R 76 " --> pdb=" O PHE R 72 " (cutoff:3.500A) Proline residue: R 77 - end of helix Processing helix chain 'R' and resid 92 through 125 removed outlier: 3.664A pdb=" N ILE R 124 " --> pdb=" O ARG R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 134 No H-bonds generated for 'chain 'R' and resid 132 through 134' Processing helix chain 'R' and resid 136 through 157 Proline residue: R 156 - end of helix Processing helix chain 'R' and resid 181 through 195 removed outlier: 3.603A pdb=" N ILE R 186 " --> pdb=" O ASN R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 197 through 216 Processing helix chain 'R' and resid 228 through 259 removed outlier: 3.563A pdb=" N VAL R 238 " --> pdb=" O VAL R 234 " (cutoff:3.500A) Proline residue: R 247 - end of helix Processing helix chain 'R' and resid 270 through 296 removed outlier: 3.558A pdb=" N VAL R 279 " --> pdb=" O SER R 275 " (cutoff:3.500A) Proline residue: R 282 - end of helix removed outlier: 4.117A pdb=" N ASN R 287 " --> pdb=" O LEU R 283 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER R 288 " --> pdb=" O ALA R 284 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL R 289 " --> pdb=" O PHE R 285 " (cutoff:3.500A) Proline residue: R 292 - end of helix Processing helix chain 'R' and resid 300 through 308 Processing sheet with id= A, first strand: chain 'A' and resid 319 through 323 removed outlier: 7.168A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.793A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.746A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.647A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 198 through 202 removed outlier: 3.545A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.421A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.396A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.773A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.938A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 146 through 148 removed outlier: 6.320A pdb=" N LYS E 244 " --> pdb=" O VAL E 147 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'E' and resid 155 through 160 Processing sheet with id= M, first strand: chain 'E' and resid 226 through 231 removed outlier: 6.259A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) 411 hydrogen bonds defined for protein. 1182 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: 2.40 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1410 1.31 - 1.44: 2459 1.44 - 1.57: 4948 1.57 - 1.69: 2 1.69 - 1.82: 78 Bond restraints: 8897 Sorted by residual: bond pdb=" CA LEU E 233 " pdb=" C LEU E 233 " ideal model delta sigma weight residual 1.524 1.451 0.073 1.32e-02 5.74e+03 3.05e+01 bond pdb=" CA LEU E 237 " pdb=" C LEU E 237 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.30e-02 5.92e+03 2.37e+01 bond pdb=" CA VAL A 233 " pdb=" C VAL A 233 " ideal model delta sigma weight residual 1.524 1.473 0.051 1.08e-02 8.57e+03 2.21e+01 bond pdb=" CA THR R 246 " pdb=" C THR R 246 " ideal model delta sigma weight residual 1.521 1.571 -0.049 1.17e-02 7.31e+03 1.77e+01 bond pdb=" C LEU E 237 " pdb=" O LEU E 237 " ideal model delta sigma weight residual 1.234 1.186 0.048 1.23e-02 6.61e+03 1.53e+01 ... (remaining 8892 not shown) Histogram of bond angle deviations from ideal: 100.42 - 107.59: 281 107.59 - 114.75: 5199 114.75 - 121.91: 4778 121.91 - 129.08: 1741 129.08 - 136.24: 62 Bond angle restraints: 12061 Sorted by residual: angle pdb=" C LYS R 229 " pdb=" N PRO R 230 " pdb=" CA PRO R 230 " ideal model delta sigma weight residual 119.05 111.98 7.07 1.11e+00 8.12e-01 4.06e+01 angle pdb=" N GLN R 270 " pdb=" CA GLN R 270 " pdb=" C GLN R 270 " ideal model delta sigma weight residual 112.23 104.57 7.66 1.26e+00 6.30e-01 3.70e+01 angle pdb=" N LEU A 232 " pdb=" CA LEU A 232 " pdb=" C LEU A 232 " ideal model delta sigma weight residual 110.55 102.91 7.64 1.35e+00 5.49e-01 3.20e+01 angle pdb=" O LYS R 229 " pdb=" C LYS R 229 " pdb=" N PRO R 230 " ideal model delta sigma weight residual 120.48 124.76 -4.28 8.90e-01 1.26e+00 2.31e+01 angle pdb=" CA LYS R 229 " pdb=" C LYS R 229 " pdb=" N PRO R 230 " ideal model delta sigma weight residual 120.77 116.60 4.17 9.70e-01 1.06e+00 1.85e+01 ... (remaining 12056 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 4725 17.91 - 35.82: 410 35.82 - 53.73: 107 53.73 - 71.63: 14 71.63 - 89.54: 8 Dihedral angle restraints: 5264 sinusoidal: 1998 harmonic: 3266 Sorted by residual: dihedral pdb=" CA LYS B 78 " pdb=" C LYS B 78 " pdb=" N LEU B 79 " pdb=" CA LEU B 79 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.83e+01 dihedral pdb=" CA GLN B 75 " pdb=" C GLN B 75 " pdb=" N ASP B 76 " pdb=" CA ASP B 76 " ideal model delta harmonic sigma weight residual 180.00 160.72 19.28 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA ARG E 191 " pdb=" C ARG E 191 " pdb=" N MET E 192 " pdb=" CA MET E 192 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 5261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1182 0.055 - 0.109: 156 0.109 - 0.164: 37 0.164 - 0.219: 1 0.219 - 0.273: 4 Chirality restraints: 1380 Sorted by residual: chirality pdb=" CA TYR E 235 " pdb=" N TYR E 235 " pdb=" C TYR E 235 " pdb=" CB TYR E 235 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CA ILE R 278 " pdb=" N ILE R 278 " pdb=" C ILE R 278 " pdb=" CB ILE R 278 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.25 2.00e-01 2.50e+01 1.54e+00 chirality pdb=" CA THR E 238 " pdb=" N THR E 238 " pdb=" C THR E 238 " pdb=" CB THR E 238 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1377 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 150 " 0.042 5.00e-02 4.00e+02 6.43e-02 6.61e+00 pdb=" N PRO E 151 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 151 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 151 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE R 245 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C PHE R 245 " -0.040 2.00e-02 2.50e+03 pdb=" O PHE R 245 " 0.015 2.00e-02 2.50e+03 pdb=" N THR R 246 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN R 291 " -0.037 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO R 292 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO R 292 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO R 292 " -0.031 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1696 2.77 - 3.30: 8534 3.30 - 3.84: 14807 3.84 - 4.37: 18289 4.37 - 4.90: 31465 Nonbonded interactions: 74791 Sorted by model distance: nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.239 2.440 nonbonded pdb=" O ASP B 195 " pdb=" OG1 THR B 196 " model vdw 2.248 2.440 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.277 2.440 nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.284 2.440 nonbonded pdb=" O ASN R 274 " pdb=" N TYR R 277 " model vdw 2.313 2.520 ... (remaining 74786 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.820 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.320 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8897 Z= 0.253 Angle : 0.652 11.238 12061 Z= 0.374 Chirality : 0.043 0.273 1380 Planarity : 0.005 0.068 1523 Dihedral : 14.747 89.543 3153 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.54 % Allowed : 15.09 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.26), residues: 1100 helix: 1.71 (0.27), residues: 383 sheet: 0.32 (0.29), residues: 307 loop : 0.27 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 88 HIS 0.005 0.001 HIS A 188 PHE 0.013 0.001 PHE R 34 TYR 0.016 0.001 TYR R 83 ARG 0.014 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 0.972 Fit side-chains REVERT: A 33 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7386 (mm-30) REVERT: B 46 ARG cc_start: 0.8073 (ptm160) cc_final: 0.7854 (ptm160) REVERT: B 219 ARG cc_start: 0.7946 (mmm160) cc_final: 0.7352 (mmt-90) REVERT: E 46 GLU cc_start: 0.8026 (tt0) cc_final: 0.7812 (tt0) REVERT: R 189 MET cc_start: 0.8267 (mmm) cc_final: 0.8018 (mmm) outliers start: 5 outliers final: 2 residues processed: 146 average time/residue: 1.3270 time to fit residues: 205.1932 Evaluate side-chains 121 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 119 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain E residue 193 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 255 ASN A 269 ASN A 331 ASN A 333 GLN B 75 GLN B 259 GLN E 3 GLN E 39 GLN E 77 ASN E 179 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8897 Z= 0.251 Angle : 0.554 9.193 12061 Z= 0.295 Chirality : 0.043 0.144 1380 Planarity : 0.004 0.040 1523 Dihedral : 4.587 33.322 1221 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.91 % Allowed : 14.44 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1100 helix: 2.06 (0.25), residues: 393 sheet: 0.34 (0.30), residues: 287 loop : 0.32 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS B 91 PHE 0.014 0.001 PHE A 274 TYR 0.013 0.001 TYR R 48 ARG 0.008 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 135 time to evaluate : 1.033 Fit side-chains REVERT: A 33 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7526 (mm-30) REVERT: B 46 ARG cc_start: 0.8079 (ptm160) cc_final: 0.7830 (ptm160) REVERT: B 214 ARG cc_start: 0.8074 (mmt-90) cc_final: 0.7838 (mmp80) REVERT: B 219 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7241 (mpt180) REVERT: B 267 ASP cc_start: 0.7802 (m-30) cc_final: 0.7487 (m-30) REVERT: E 46 GLU cc_start: 0.7935 (tt0) cc_final: 0.7726 (tt0) REVERT: E 160 ARG cc_start: 0.7751 (ttm110) cc_final: 0.7536 (ttm110) REVERT: R 193 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7549 (tt) REVERT: R 253 ASN cc_start: 0.8757 (m-40) cc_final: 0.8511 (m-40) outliers start: 27 outliers final: 12 residues processed: 147 average time/residue: 1.2295 time to fit residues: 192.0600 Evaluate side-chains 133 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 149 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 234 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 108 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 269 ASN A 311 ASN A 331 ASN B 75 GLN B 259 GLN E 3 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8897 Z= 0.350 Angle : 0.581 10.313 12061 Z= 0.309 Chirality : 0.045 0.157 1380 Planarity : 0.004 0.048 1523 Dihedral : 4.497 21.105 1218 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.88 % Allowed : 15.84 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1100 helix: 2.03 (0.25), residues: 394 sheet: 0.25 (0.30), residues: 297 loop : 0.26 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.005 0.001 HIS G 44 PHE 0.015 0.002 PHE R 115 TYR 0.013 0.002 TYR R 107 ARG 0.006 0.001 ARG R 255 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 136 time to evaluate : 1.070 Fit side-chains REVERT: A 195 HIS cc_start: 0.6731 (t-170) cc_final: 0.6497 (t-90) REVERT: B 219 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7285 (mpt180) REVERT: E 46 GLU cc_start: 0.8022 (tt0) cc_final: 0.7811 (tt0) REVERT: R 193 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7642 (tt) REVERT: R 253 ASN cc_start: 0.8786 (m-40) cc_final: 0.8524 (m-40) outliers start: 36 outliers final: 17 residues processed: 155 average time/residue: 1.1661 time to fit residues: 192.8652 Evaluate side-chains 147 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 128 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 234 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 269 ASN A 331 ASN B 75 GLN B 259 GLN E 3 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8897 Z= 0.233 Angle : 0.534 10.087 12061 Z= 0.283 Chirality : 0.042 0.160 1380 Planarity : 0.004 0.056 1523 Dihedral : 4.280 20.476 1218 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.77 % Allowed : 16.92 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.25), residues: 1100 helix: 2.25 (0.25), residues: 393 sheet: 0.26 (0.30), residues: 288 loop : 0.15 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 82 HIS 0.009 0.001 HIS B 266 PHE 0.011 0.001 PHE R 115 TYR 0.017 0.001 TYR R 48 ARG 0.009 0.001 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 140 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: B 219 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7279 (mpt180) REVERT: E 160 ARG cc_start: 0.7724 (ttm110) cc_final: 0.7423 (ttm110) REVERT: R 193 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7706 (tt) REVERT: R 253 ASN cc_start: 0.8751 (m-40) cc_final: 0.8483 (m-40) outliers start: 35 outliers final: 14 residues processed: 159 average time/residue: 1.1113 time to fit residues: 188.8803 Evaluate side-chains 141 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 193 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.1980 chunk 43 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 269 ASN B 75 GLN E 3 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8897 Z= 0.206 Angle : 0.516 9.275 12061 Z= 0.273 Chirality : 0.042 0.169 1380 Planarity : 0.004 0.051 1523 Dihedral : 4.137 20.389 1218 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.59 % Allowed : 19.50 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.25), residues: 1100 helix: 2.35 (0.25), residues: 393 sheet: 0.33 (0.30), residues: 280 loop : 0.03 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.007 0.001 HIS B 266 PHE 0.011 0.001 PHE R 115 TYR 0.018 0.001 TYR R 48 ARG 0.006 0.000 ARG R 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.027 Fit side-chains REVERT: A 32 ARG cc_start: 0.8026 (mtt90) cc_final: 0.7733 (mpt90) REVERT: A 252 SER cc_start: 0.8670 (m) cc_final: 0.8401 (m) REVERT: B 219 ARG cc_start: 0.7971 (mmm160) cc_final: 0.7266 (mpt180) REVERT: B 267 ASP cc_start: 0.7861 (m-30) cc_final: 0.7659 (m-30) REVERT: E 160 ARG cc_start: 0.7699 (ttm110) cc_final: 0.7423 (ttm110) REVERT: R 253 ASN cc_start: 0.8726 (m-40) cc_final: 0.8487 (m-40) outliers start: 24 outliers final: 13 residues processed: 148 average time/residue: 1.1160 time to fit residues: 176.7180 Evaluate side-chains 136 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 16 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 21 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 55 optimal weight: 0.2980 chunk 102 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 269 ASN B 75 GLN E 3 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8897 Z= 0.204 Angle : 0.525 9.741 12061 Z= 0.274 Chirality : 0.042 0.163 1380 Planarity : 0.004 0.048 1523 Dihedral : 4.073 19.583 1218 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.91 % Allowed : 20.26 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1100 helix: 2.43 (0.25), residues: 393 sheet: 0.29 (0.29), residues: 285 loop : 0.04 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS B 266 PHE 0.011 0.001 PHE R 115 TYR 0.015 0.001 TYR R 48 ARG 0.006 0.000 ARG R 255 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.066 Fit side-chains REVERT: A 32 ARG cc_start: 0.8024 (mtt90) cc_final: 0.7732 (mpt90) REVERT: A 252 SER cc_start: 0.8674 (m) cc_final: 0.8410 (m) REVERT: A 297 GLU cc_start: 0.8282 (mm-30) cc_final: 0.8059 (tt0) REVERT: B 219 ARG cc_start: 0.7970 (mmm160) cc_final: 0.7259 (mpt180) REVERT: B 267 ASP cc_start: 0.7849 (m-30) cc_final: 0.7638 (m-30) REVERT: E 160 ARG cc_start: 0.7656 (ttm110) cc_final: 0.7410 (ttm110) REVERT: R 193 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7715 (tt) REVERT: R 253 ASN cc_start: 0.8782 (m-40) cc_final: 0.8556 (m-40) outliers start: 27 outliers final: 18 residues processed: 148 average time/residue: 1.1878 time to fit residues: 187.4581 Evaluate side-chains 145 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 234 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 66 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 269 ASN B 75 GLN E 3 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8897 Z= 0.237 Angle : 0.537 9.419 12061 Z= 0.280 Chirality : 0.042 0.171 1380 Planarity : 0.004 0.046 1523 Dihedral : 4.125 19.734 1218 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.12 % Allowed : 20.58 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.25), residues: 1100 helix: 2.40 (0.26), residues: 393 sheet: 0.29 (0.30), residues: 288 loop : 0.04 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.008 0.001 HIS B 266 PHE 0.012 0.001 PHE R 115 TYR 0.018 0.001 TYR R 48 ARG 0.007 0.000 ARG R 255 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 1.066 Fit side-chains REVERT: A 32 ARG cc_start: 0.7965 (mtt90) cc_final: 0.7642 (mpt90) REVERT: A 297 GLU cc_start: 0.8281 (mm-30) cc_final: 0.8064 (tt0) REVERT: B 219 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7246 (mpt180) REVERT: R 193 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7714 (tt) REVERT: R 253 ASN cc_start: 0.8786 (m-40) cc_final: 0.8557 (m-40) outliers start: 29 outliers final: 21 residues processed: 144 average time/residue: 1.2023 time to fit residues: 184.3556 Evaluate side-chains 145 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 219 ARG Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 69 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 186 ILE Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 234 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A 269 ASN B 75 GLN E 3 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8897 Z= 0.189 Angle : 0.526 11.210 12061 Z= 0.275 Chirality : 0.042 0.170 1380 Planarity : 0.004 0.046 1523 Dihedral : 4.034 19.151 1218 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.80 % Allowed : 21.44 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.25), residues: 1100 helix: 2.47 (0.26), residues: 393 sheet: 0.29 (0.30), residues: 285 loop : 0.04 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.007 0.001 HIS B 266 PHE 0.010 0.001 PHE R 115 TYR 0.018 0.001 TYR R 48 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 1.082 Fit side-chains REVERT: A 32 ARG cc_start: 0.7936 (mtt90) cc_final: 0.7631 (mpt90) REVERT: A 252 SER cc_start: 0.8666 (m) cc_final: 0.8413 (m) REVERT: A 269 ASN cc_start: 0.9101 (m-40) cc_final: 0.8835 (m110) REVERT: A 297 GLU cc_start: 0.8274 (mm-30) cc_final: 0.8057 (tt0) REVERT: A 298 GLU cc_start: 0.8066 (tt0) cc_final: 0.7687 (tt0) REVERT: B 219 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7222 (mmt-90) REVERT: E 160 ARG cc_start: 0.7672 (ttm110) cc_final: 0.7463 (ttm110) REVERT: G 48 ASP cc_start: 0.8108 (t0) cc_final: 0.7896 (t0) REVERT: R 193 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7746 (tt) REVERT: R 253 ASN cc_start: 0.8740 (m-40) cc_final: 0.8537 (m-40) outliers start: 26 outliers final: 18 residues processed: 148 average time/residue: 1.2241 time to fit residues: 193.0729 Evaluate side-chains 143 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 234 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.0170 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.4980 chunk 89 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 75 GLN E 3 GLN E 77 ASN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 8897 Z= 0.188 Angle : 0.520 8.440 12061 Z= 0.271 Chirality : 0.042 0.175 1380 Planarity : 0.004 0.051 1523 Dihedral : 4.009 19.178 1218 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.48 % Allowed : 21.98 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.25), residues: 1100 helix: 2.52 (0.26), residues: 392 sheet: 0.32 (0.30), residues: 276 loop : -0.01 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS B 266 PHE 0.010 0.001 PHE R 115 TYR 0.018 0.001 TYR R 30 ARG 0.008 0.000 ARG E 160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 132 time to evaluate : 0.926 Fit side-chains REVERT: A 32 ARG cc_start: 0.7891 (mtt90) cc_final: 0.7582 (mpt90) REVERT: A 252 SER cc_start: 0.8687 (m) cc_final: 0.8439 (m) REVERT: B 219 ARG cc_start: 0.7923 (mmm160) cc_final: 0.7211 (mmt-90) REVERT: E 87 ARG cc_start: 0.7518 (mtm-85) cc_final: 0.6934 (mtp85) REVERT: G 48 ASP cc_start: 0.8130 (t0) cc_final: 0.7914 (t0) REVERT: R 193 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7730 (tt) outliers start: 23 outliers final: 20 residues processed: 146 average time/residue: 1.1587 time to fit residues: 180.8135 Evaluate side-chains 148 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 127 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 109 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 87 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.3980 chunk 53 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 75 GLN E 3 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8897 Z= 0.172 Angle : 0.525 11.217 12061 Z= 0.272 Chirality : 0.041 0.171 1380 Planarity : 0.004 0.043 1523 Dihedral : 3.921 19.062 1218 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.26 % Allowed : 22.84 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1100 helix: 2.58 (0.26), residues: 391 sheet: 0.32 (0.30), residues: 276 loop : 0.07 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.007 0.001 HIS B 266 PHE 0.010 0.001 PHE R 34 TYR 0.016 0.001 TYR R 48 ARG 0.010 0.000 ARG E 160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.048 Fit side-chains REVERT: A 32 ARG cc_start: 0.7887 (mtt90) cc_final: 0.7583 (mpt90) REVERT: A 252 SER cc_start: 0.8681 (m) cc_final: 0.8436 (m) REVERT: B 219 ARG cc_start: 0.7919 (mmm160) cc_final: 0.7182 (mmt-90) REVERT: E 87 ARG cc_start: 0.7567 (mtm-85) cc_final: 0.6963 (mtp85) REVERT: E 160 ARG cc_start: 0.7747 (ttm110) cc_final: 0.7514 (tpp-160) REVERT: G 48 ASP cc_start: 0.8107 (t0) cc_final: 0.7902 (t0) REVERT: R 193 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7806 (tt) outliers start: 21 outliers final: 16 residues processed: 146 average time/residue: 1.1903 time to fit residues: 185.4254 Evaluate side-chains 146 residues out of total 971 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 261 ASP Chi-restraints excluded: chain A residue 313 ARG Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 96 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain R residue 79 LEU Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 234 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 87 optimal weight: 4.9990 chunk 36 optimal weight: 0.3980 chunk 89 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 76 optimal weight: 0.0570 chunk 4 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN B 75 GLN E 3 GLN ** R 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.163153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.115929 restraints weight = 9877.745| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.24 r_work: 0.3227 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 8897 Z= 0.149 Angle : 0.505 11.056 12061 Z= 0.264 Chirality : 0.041 0.165 1380 Planarity : 0.003 0.043 1523 Dihedral : 3.786 19.050 1218 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.83 % Allowed : 23.28 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.25), residues: 1100 helix: 2.61 (0.26), residues: 391 sheet: 0.37 (0.30), residues: 276 loop : 0.07 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 82 HIS 0.007 0.001 HIS B 266 PHE 0.009 0.001 PHE R 34 TYR 0.016 0.001 TYR R 48 ARG 0.007 0.000 ARG R 255 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3777.65 seconds wall clock time: 66 minutes 33.47 seconds (3993.47 seconds total)