Starting phenix.real_space_refine on Wed Feb 14 23:41:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9y_31500/02_2024/7f9y_31500_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9y_31500/02_2024/7f9y_31500.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9y_31500/02_2024/7f9y_31500.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9y_31500/02_2024/7f9y_31500.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9y_31500/02_2024/7f9y_31500_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f9y_31500/02_2024/7f9y_31500_neut_updated.pdb" } resolution = 2.9 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= 0.002 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2178 atoms to isotropic. 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 54 5.16 5 C 5329 2.51 5 N 1439 2.21 5 O 1532 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 61": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "C ARG 10": "NH1" <-> "NH2" Residue "C ARG 14": "NH1" <-> "NH2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N ARG 19": "NH1" <-> "NH2" Residue "R ARG 72": "NH1" <-> "NH2" Residue "R ARG 75": "NH1" <-> "NH2" Residue "R ARG 107": "NH1" <-> "NH2" Residue "R PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 141": "NH1" <-> "NH2" Residue "R ARG 150": "NH1" <-> "NH2" Residue "R GLU 197": "OE1" <-> "OE2" Residue "R ARG 206": "NH1" <-> "NH2" Residue "R ARG 237": "NH1" <-> "NH2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R PHE 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "R GLU 291": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8354 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1877 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 123 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 2280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2280 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 1 Chain: "C" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'OCA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'OCA:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.13, per 1000 atoms: 0.61 Number of scatterers: 8354 At special positions: 0 Unit cell: (88.893, 111.384, 127.449, 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 54 16.00 O 1532 8.00 N 1439 7.00 C 5329 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 116 " - pdb=" SG CYS R 198 " distance=2.04 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.7 seconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1980 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 32 helices and 11 sheets defined 39.8% alpha, 20.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.90 Creating SS restraints... Processing helix chain 'A' and resid 17 through 39 removed outlier: 3.744A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ASP A 33 " --> pdb=" O GLN A 29 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 231 through 237 removed outlier: 4.782A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N CYS A 237 " --> pdb=" O LYS A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.538A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 390 removed outlier: 4.024A pdb=" N ALA A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.184A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 13 removed outlier: 4.305A pdb=" N GLN C 9 " --> pdb=" O PRO C 6 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 11 " --> pdb=" O HIS C 8 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N GLN C 12 " --> pdb=" O GLN C 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.585A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) 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 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 40 through 70 removed outlier: 3.686A pdb=" N ARG R 70 " --> pdb=" O LEU R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 104 removed outlier: 3.644A pdb=" N CYS R 95 " --> pdb=" O LEU R 91 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N MET R 96 " --> pdb=" O ILE R 92 " (cutoff:3.500A) Proline residue: R 97 - end of helix Processing helix chain 'R' and resid 113 through 146 Processing helix chain 'R' and resid 148 through 153 removed outlier: 4.403A pdb=" N LYS R 152 " --> pdb=" O PRO R 148 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N VAL R 153 " --> pdb=" O LEU R 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 148 through 153' Processing helix chain 'R' and resid 157 through 181 Proline residue: R 177 - end of helix removed outlier: 4.635A pdb=" N VAL R 180 " --> pdb=" O GLY R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 192 through 194 No H-bonds generated for 'chain 'R' and resid 192 through 194' Processing helix chain 'R' and resid 202 through 206 Processing helix chain 'R' and resid 210 through 213 No H-bonds generated for 'chain 'R' and resid 210 through 213' Processing helix chain 'R' and resid 215 through 218 No H-bonds generated for 'chain 'R' and resid 215 through 218' Processing helix chain 'R' and resid 222 through 240 removed outlier: 3.606A pdb=" N TYR R 232 " --> pdb=" O LEU R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 258 through 290 Proline residue: R 278 - end of helix removed outlier: 3.909A pdb=" N PHE R 290 " --> pdb=" O PHE R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 322 removed outlier: 3.739A pdb=" N TYR R 313 " --> pdb=" O PHE R 309 " (cutoff:3.500A) Proline residue: R 320 - end of helix Processing helix chain 'R' and resid 328 through 333 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.113A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.904A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.235A 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: 6.828A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS B 121 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.275A 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: 6.603A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.159A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 200 " --> pdb=" O SER B 191 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.441A 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: 6.523A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 276 through 278 removed outlier: 3.522A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.546A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.516A pdb=" N GLN N 3 " --> pdb=" O SER N 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER N 25 " --> pdb=" O GLN N 3 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.768A pdb=" N SER N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 182 through 185 383 hydrogen bonds defined for protein. 1050 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: 2.54 Time building geometry restraints manager: 3.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1347 1.31 - 1.44: 2332 1.44 - 1.57: 4774 1.57 - 1.70: 0 1.70 - 1.83: 75 Bond restraints: 8528 Sorted by residual: bond pdb=" C1 OCA C 101 " pdb=" O1 OCA C 101 " ideal model delta sigma weight residual 1.247 1.185 0.062 2.00e-02 2.50e+03 9.70e+00 bond pdb=" N GLY C 0 " pdb=" CA GLY C 0 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.25e+00 bond pdb=" C13 CLR R 602 " pdb=" C17 CLR R 602 " ideal model delta sigma weight residual 1.550 1.513 0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C13 CLR R 601 " pdb=" C17 CLR R 601 " ideal model delta sigma weight residual 1.550 1.515 0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" N GLU A 15 " pdb=" CA GLU A 15 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 ... (remaining 8523 not shown) Histogram of bond angle deviations from ideal: 100.37 - 107.12: 199 107.12 - 113.87: 4828 113.87 - 120.61: 3440 120.61 - 127.36: 3004 127.36 - 134.10: 88 Bond angle restraints: 11559 Sorted by residual: angle pdb=" C13 CLR R 601 " pdb=" C17 CLR R 601 " pdb=" C20 CLR R 601 " ideal model delta sigma weight residual 119.60 111.03 8.57 3.00e+00 1.11e-01 8.17e+00 angle pdb=" N LEU R 295 " pdb=" CA LEU R 295 " pdb=" C LEU R 295 " ideal model delta sigma weight residual 114.56 111.04 3.52 1.27e+00 6.20e-01 7.67e+00 angle pdb=" C LEU R 118 " pdb=" N PHE R 119 " pdb=" CA PHE R 119 " ideal model delta sigma weight residual 120.68 116.14 4.54 1.70e+00 3.46e-01 7.14e+00 angle pdb=" N PHE R 119 " pdb=" CA PHE R 119 " pdb=" CB PHE R 119 " ideal model delta sigma weight residual 110.30 114.28 -3.98 1.54e+00 4.22e-01 6.68e+00 angle pdb=" C13 CLR R 602 " pdb=" C17 CLR R 602 " pdb=" C20 CLR R 602 " ideal model delta sigma weight residual 119.60 111.85 7.75 3.00e+00 1.11e-01 6.68e+00 ... (remaining 11554 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.34: 4747 17.34 - 34.68: 361 34.68 - 52.02: 51 52.02 - 69.36: 14 69.36 - 86.70: 5 Dihedral angle restraints: 5178 sinusoidal: 2124 harmonic: 3054 Sorted by residual: dihedral pdb=" CA PRO R 39 " pdb=" C PRO R 39 " pdb=" N ALA R 40 " pdb=" CA ALA R 40 " ideal model delta harmonic sigma weight residual -180.00 -161.52 -18.48 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA SER R 218 " pdb=" C SER R 218 " pdb=" N ILE R 219 " pdb=" CA ILE R 219 " ideal model delta harmonic sigma weight residual 180.00 162.67 17.33 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA ASP A 252 " pdb=" CB ASP A 252 " pdb=" CG ASP A 252 " pdb=" OD1 ASP A 252 " ideal model delta sinusoidal sigma weight residual -30.00 -85.93 55.93 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 5175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1184 0.067 - 0.134: 124 0.134 - 0.201: 3 0.201 - 0.268: 2 0.268 - 0.335: 2 Chirality restraints: 1315 Sorted by residual: chirality pdb=" C13 CLR R 601 " pdb=" C12 CLR R 601 " pdb=" C14 CLR R 601 " pdb=" C17 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.93 -2.60 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C13 CLR R 602 " pdb=" C12 CLR R 602 " pdb=" C14 CLR R 602 " pdb=" C17 CLR R 602 " both_signs ideal model delta sigma weight residual False -2.93 -2.61 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1312 not shown) Planarity restraints: 1458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO N 88 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.021 5.00e-02 4.00e+02 3.19e-02 1.62e+00 pdb=" N PRO B 236 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE R 38 " -0.021 5.00e-02 4.00e+02 3.18e-02 1.62e+00 pdb=" N PRO R 39 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO R 39 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 39 " -0.018 5.00e-02 4.00e+02 ... (remaining 1455 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 56 2.54 - 3.13: 6626 3.13 - 3.72: 12830 3.72 - 4.31: 17746 4.31 - 4.90: 30747 Nonbonded interactions: 68005 Sorted by model distance: nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 1.951 2.440 nonbonded pdb=" O HIS B 54 " pdb=" OG SER B 334 " model vdw 2.148 2.440 nonbonded pdb=" OG1 THR R 77 " pdb=" OE2 GLU R 140 " model vdw 2.156 2.440 nonbonded pdb=" O PHE G 61 " pdb=" NE ARG G 62 " model vdw 2.158 2.520 nonbonded pdb=" OH TYR R 106 " pdb=" OE1 GLU R 197 " model vdw 2.233 2.440 ... (remaining 68000 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 2.200 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.880 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8528 Z= 0.180 Angle : 0.551 8.573 11559 Z= 0.306 Chirality : 0.042 0.335 1315 Planarity : 0.003 0.041 1458 Dihedral : 12.549 86.698 3195 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.27), residues: 1033 helix: 1.99 (0.27), residues: 410 sheet: 1.12 (0.35), residues: 214 loop : 0.51 (0.33), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 281 HIS 0.003 0.001 HIS A 357 PHE 0.010 0.001 PHE A 363 TYR 0.007 0.001 TYR R 330 ARG 0.013 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 204 time to evaluate : 0.889 Fit side-chains REVERT: A 29 GLN cc_start: 0.7971 (tp40) cc_final: 0.7717 (mm-40) REVERT: A 221 MET cc_start: 0.8257 (ttp) cc_final: 0.8023 (ttm) REVERT: A 272 ASP cc_start: 0.7143 (m-30) cc_final: 0.6729 (m-30) REVERT: A 284 THR cc_start: 0.8369 (p) cc_final: 0.7905 (t) REVERT: A 336 ARG cc_start: 0.7692 (ttp80) cc_final: 0.7419 (ttt-90) REVERT: A 390 GLU cc_start: 0.6389 (mm-30) cc_final: 0.6152 (mm-30) REVERT: B 214 ARG cc_start: 0.6944 (mpt-90) cc_final: 0.6736 (mmm-85) REVERT: N 29 PHE cc_start: 0.8446 (t80) cc_final: 0.8118 (t80) REVERT: R 85 MET cc_start: 0.7284 (ttm) cc_final: 0.7073 (mtp) outliers start: 0 outliers final: 0 residues processed: 204 average time/residue: 1.2658 time to fit residues: 273.6926 Evaluate side-chains 175 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN B 220 GLN B 268 ASN N 31 ASN N 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8528 Z= 0.230 Angle : 0.557 7.353 11559 Z= 0.290 Chirality : 0.043 0.151 1315 Planarity : 0.005 0.048 1458 Dihedral : 5.804 59.582 1277 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.21 % Allowed : 9.59 % Favored : 88.20 % 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: 1.45 (0.26), residues: 1033 helix: 1.59 (0.26), residues: 406 sheet: 1.33 (0.35), residues: 205 loop : 0.25 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 47 HIS 0.007 0.001 HIS A 357 PHE 0.019 0.002 PHE R 279 TYR 0.015 0.001 TYR B 59 ARG 0.011 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 182 time to evaluate : 0.976 Fit side-chains REVERT: A 29 GLN cc_start: 0.7997 (tp40) cc_final: 0.7768 (mm-40) REVERT: A 218 ASN cc_start: 0.8194 (m-40) cc_final: 0.7784 (m110) REVERT: A 221 MET cc_start: 0.8246 (ttp) cc_final: 0.7997 (ttm) REVERT: A 266 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7529 (tt) REVERT: A 272 ASP cc_start: 0.7126 (m-30) cc_final: 0.6762 (m-30) REVERT: B 197 ARG cc_start: 0.7174 (mmm-85) cc_final: 0.6766 (mmm-85) REVERT: B 214 ARG cc_start: 0.7164 (mpt-90) cc_final: 0.6714 (mpp80) REVERT: B 219 ARG cc_start: 0.7786 (mtt-85) cc_final: 0.7548 (mmm-85) REVERT: B 262 MET cc_start: 0.7075 (tpp) cc_final: 0.6605 (tpp) REVERT: G 47 GLU cc_start: 0.7490 (tt0) cc_final: 0.7253 (tt0) REVERT: N 29 PHE cc_start: 0.8548 (t80) cc_final: 0.8172 (t80) REVERT: N 38 ARG cc_start: 0.8519 (ptt180) cc_final: 0.8300 (ptt180) REVERT: R 65 MET cc_start: 0.6757 (tmm) cc_final: 0.5690 (tmm) REVERT: R 326 MET cc_start: 0.6952 (mmm) cc_final: 0.6726 (mmm) outliers start: 20 outliers final: 9 residues processed: 191 average time/residue: 1.2460 time to fit residues: 253.0877 Evaluate side-chains 186 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 176 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 119 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 0.0010 chunk 90 optimal weight: 3.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8528 Z= 0.177 Angle : 0.498 7.420 11559 Z= 0.262 Chirality : 0.041 0.143 1315 Planarity : 0.004 0.046 1458 Dihedral : 5.430 48.164 1277 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.43 % Allowed : 13.78 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.26), residues: 1033 helix: 1.46 (0.26), residues: 405 sheet: 1.25 (0.35), residues: 204 loop : -0.00 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.006 0.001 HIS A 357 PHE 0.015 0.001 PHE R 279 TYR 0.010 0.001 TYR B 59 ARG 0.010 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 182 time to evaluate : 0.913 Fit side-chains REVERT: A 29 GLN cc_start: 0.8004 (tp40) cc_final: 0.7757 (mm-40) REVERT: A 39 ARG cc_start: 0.7792 (ptp-110) cc_final: 0.7509 (mtm110) REVERT: A 272 ASP cc_start: 0.7125 (m-30) cc_final: 0.6751 (m-30) REVERT: B 78 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7693 (mttp) REVERT: B 197 ARG cc_start: 0.7287 (mmm-85) cc_final: 0.6386 (mmm-85) REVERT: B 214 ARG cc_start: 0.7262 (mpt-90) cc_final: 0.6757 (mpp80) REVERT: B 219 ARG cc_start: 0.7870 (mtt-85) cc_final: 0.7609 (mmm-85) REVERT: B 262 MET cc_start: 0.7069 (tpp) cc_final: 0.6545 (tpp) REVERT: B 335 PHE cc_start: 0.8593 (m-10) cc_final: 0.8166 (m-80) REVERT: G 47 GLU cc_start: 0.7468 (tt0) cc_final: 0.7216 (tt0) REVERT: N 29 PHE cc_start: 0.8582 (t80) cc_final: 0.8147 (t80) REVERT: R 65 MET cc_start: 0.6782 (tmm) cc_final: 0.5729 (tmm) REVERT: R 85 MET cc_start: 0.7368 (mtp) cc_final: 0.7147 (mtm) REVERT: R 326 MET cc_start: 0.6924 (mmm) cc_final: 0.6622 (mmm) outliers start: 22 outliers final: 12 residues processed: 190 average time/residue: 1.2818 time to fit residues: 258.5209 Evaluate side-chains 191 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 178 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 306 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 97 optimal weight: 0.4980 chunk 48 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 81 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8528 Z= 0.196 Angle : 0.510 8.542 11559 Z= 0.267 Chirality : 0.041 0.146 1315 Planarity : 0.005 0.068 1458 Dihedral : 5.321 46.671 1277 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.98 % Allowed : 14.77 % Favored : 82.25 % 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: 1.13 (0.26), residues: 1033 helix: 1.53 (0.26), residues: 399 sheet: 1.14 (0.35), residues: 208 loop : -0.12 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.018 0.001 PHE R 119 TYR 0.010 0.001 TYR B 59 ARG 0.014 0.001 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 180 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8030 (tp40) cc_final: 0.7755 (mm-40) REVERT: A 33 ASP cc_start: 0.7274 (p0) cc_final: 0.7015 (p0) REVERT: A 39 ARG cc_start: 0.7726 (ptp-110) cc_final: 0.7493 (mtm110) REVERT: A 272 ASP cc_start: 0.7131 (m-30) cc_final: 0.6759 (m-30) REVERT: B 49 ARG cc_start: 0.7997 (mmt-90) cc_final: 0.7693 (mmt90) REVERT: B 114 CYS cc_start: 0.7276 (p) cc_final: 0.6982 (p) REVERT: B 219 ARG cc_start: 0.7872 (mtt-85) cc_final: 0.7625 (mmm-85) REVERT: B 262 MET cc_start: 0.7092 (tpp) cc_final: 0.6560 (tpp) REVERT: B 335 PHE cc_start: 0.8646 (m-10) cc_final: 0.8271 (m-80) REVERT: G 47 GLU cc_start: 0.7482 (tt0) cc_final: 0.7217 (tt0) REVERT: N 29 PHE cc_start: 0.8615 (t80) cc_final: 0.8219 (t80) REVERT: R 65 MET cc_start: 0.6814 (tmm) cc_final: 0.5774 (tmm) REVERT: R 85 MET cc_start: 0.7345 (mtp) cc_final: 0.7123 (mtm) REVERT: R 199 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7360 (ptt90) REVERT: R 326 MET cc_start: 0.6823 (mmm) cc_final: 0.6479 (mmm) outliers start: 27 outliers final: 13 residues processed: 191 average time/residue: 1.3274 time to fit residues: 268.2797 Evaluate side-chains 187 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 173 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 199 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 67 optimal weight: 0.0970 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8528 Z= 0.207 Angle : 0.493 7.310 11559 Z= 0.261 Chirality : 0.041 0.141 1315 Planarity : 0.004 0.045 1458 Dihedral : 5.301 50.491 1277 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.09 % Allowed : 14.88 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1033 helix: 1.51 (0.26), residues: 399 sheet: 0.91 (0.35), residues: 212 loop : -0.12 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.001 PHE R 119 TYR 0.009 0.001 TYR R 81 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 179 time to evaluate : 0.880 Fit side-chains REVERT: A 29 GLN cc_start: 0.7960 (tp40) cc_final: 0.7628 (mm-40) REVERT: A 33 ASP cc_start: 0.7206 (p0) cc_final: 0.6948 (p0) REVERT: A 39 ARG cc_start: 0.7657 (ptp-110) cc_final: 0.7450 (mtm110) REVERT: A 270 LEU cc_start: 0.8248 (mt) cc_final: 0.8036 (mp) REVERT: A 272 ASP cc_start: 0.7083 (m-30) cc_final: 0.6727 (m-30) REVERT: B 197 ARG cc_start: 0.7424 (mmm-85) cc_final: 0.6475 (mmm-85) REVERT: B 214 ARG cc_start: 0.7404 (mpt-90) cc_final: 0.7001 (mpp80) REVERT: B 219 ARG cc_start: 0.7862 (mtt-85) cc_final: 0.7614 (mmm-85) REVERT: B 262 MET cc_start: 0.7118 (tpp) cc_final: 0.6606 (tpp) REVERT: B 335 PHE cc_start: 0.8663 (m-10) cc_final: 0.8265 (m-80) REVERT: G 47 GLU cc_start: 0.7492 (tt0) cc_final: 0.7220 (tt0) REVERT: N 29 PHE cc_start: 0.8586 (t80) cc_final: 0.8154 (t80) REVERT: R 65 MET cc_start: 0.6832 (tmm) cc_final: 0.5766 (tmm) REVERT: R 85 MET cc_start: 0.7498 (mtp) cc_final: 0.7281 (mtp) REVERT: R 102 ARG cc_start: 0.8292 (ttp-170) cc_final: 0.8074 (ttp-170) REVERT: R 199 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7381 (ptt90) REVERT: R 326 MET cc_start: 0.6837 (mmm) cc_final: 0.6501 (mmm) outliers start: 28 outliers final: 15 residues processed: 187 average time/residue: 1.2798 time to fit residues: 253.9879 Evaluate side-chains 182 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 166 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 199 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8528 Z= 0.212 Angle : 0.502 7.897 11559 Z= 0.262 Chirality : 0.041 0.186 1315 Planarity : 0.004 0.045 1458 Dihedral : 5.295 51.967 1277 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.98 % Allowed : 16.21 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1033 helix: 1.49 (0.27), residues: 399 sheet: 0.74 (0.35), residues: 218 loop : -0.14 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE R 119 TYR 0.009 0.001 TYR R 303 ARG 0.009 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 0.967 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7953 (tp40) cc_final: 0.7631 (mm-40) REVERT: A 33 ASP cc_start: 0.7226 (p0) cc_final: 0.6972 (p0) REVERT: A 272 ASP cc_start: 0.7099 (m-30) cc_final: 0.6738 (m-30) REVERT: B 188 MET cc_start: 0.7723 (mmm) cc_final: 0.7454 (mmp) REVERT: B 219 ARG cc_start: 0.7850 (mtt-85) cc_final: 0.7609 (mmm-85) REVERT: B 262 MET cc_start: 0.7091 (tpp) cc_final: 0.6601 (tpp) REVERT: B 335 PHE cc_start: 0.8661 (m-10) cc_final: 0.8233 (m-80) REVERT: G 47 GLU cc_start: 0.7482 (tt0) cc_final: 0.7245 (tt0) REVERT: R 65 MET cc_start: 0.6822 (tmm) cc_final: 0.5769 (tmm) REVERT: R 91 LEU cc_start: 0.7579 (tt) cc_final: 0.7373 (tp) REVERT: R 199 ARG cc_start: 0.7687 (OUTLIER) cc_final: 0.7392 (ptt90) REVERT: R 318 ILE cc_start: 0.7683 (OUTLIER) cc_final: 0.7339 (tt) REVERT: R 326 MET cc_start: 0.6850 (mmm) cc_final: 0.6520 (mmm) outliers start: 27 outliers final: 16 residues processed: 173 average time/residue: 1.2213 time to fit residues: 224.7799 Evaluate side-chains 175 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 157 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 318 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 0.0770 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 220 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8528 Z= 0.215 Angle : 0.505 7.330 11559 Z= 0.265 Chirality : 0.041 0.149 1315 Planarity : 0.004 0.045 1458 Dihedral : 5.325 53.258 1277 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.09 % Allowed : 16.43 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.26), residues: 1033 helix: 1.48 (0.27), residues: 395 sheet: 0.81 (0.35), residues: 216 loop : -0.16 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.018 0.002 PHE R 87 TYR 0.011 0.001 TYR R 303 ARG 0.011 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 160 time to evaluate : 1.040 Fit side-chains revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7962 (tp40) cc_final: 0.7660 (mm-40) REVERT: A 33 ASP cc_start: 0.7200 (p0) cc_final: 0.6929 (p0) REVERT: A 39 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7327 (ttp-110) REVERT: A 272 ASP cc_start: 0.7117 (m-30) cc_final: 0.6772 (m-30) REVERT: B 46 ARG cc_start: 0.7303 (mtp85) cc_final: 0.7088 (mtp-110) REVERT: B 188 MET cc_start: 0.7686 (mmm) cc_final: 0.7434 (mmp) REVERT: B 197 ARG cc_start: 0.7422 (mmm-85) cc_final: 0.7108 (mtp180) REVERT: B 217 MET cc_start: 0.7704 (ptm) cc_final: 0.7472 (ptm) REVERT: B 219 ARG cc_start: 0.7847 (mtt-85) cc_final: 0.7603 (mmm-85) REVERT: B 304 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7782 (ttp-170) REVERT: B 335 PHE cc_start: 0.8668 (m-10) cc_final: 0.8218 (m-80) REVERT: G 47 GLU cc_start: 0.7469 (tt0) cc_final: 0.7248 (tt0) REVERT: R 65 MET cc_start: 0.6831 (tmm) cc_final: 0.5775 (tmm) REVERT: R 199 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7391 (ptt90) REVERT: R 318 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7237 (tt) REVERT: R 326 MET cc_start: 0.6860 (mmm) cc_final: 0.6511 (mmm) outliers start: 28 outliers final: 19 residues processed: 173 average time/residue: 1.2730 time to fit residues: 233.9757 Evaluate side-chains 190 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 193 TRP Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 308 SER Chi-restraints excluded: chain R residue 318 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 0.0870 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 220 GLN B 268 ASN R 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8528 Z= 0.187 Angle : 0.495 7.713 11559 Z= 0.258 Chirality : 0.041 0.139 1315 Planarity : 0.004 0.044 1458 Dihedral : 5.255 54.548 1277 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.20 % Allowed : 16.98 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1033 helix: 1.54 (0.27), residues: 394 sheet: 0.82 (0.35), residues: 210 loop : -0.22 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.021 0.001 PHE R 87 TYR 0.020 0.001 TYR N 60 ARG 0.008 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 0.968 Fit side-chains REVERT: A 29 GLN cc_start: 0.7958 (tp40) cc_final: 0.7647 (mm-40) REVERT: A 33 ASP cc_start: 0.7095 (p0) cc_final: 0.6816 (p0) REVERT: A 39 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7328 (ttp-110) REVERT: A 272 ASP cc_start: 0.7128 (m-30) cc_final: 0.6762 (m-30) REVERT: B 46 ARG cc_start: 0.7291 (mtp85) cc_final: 0.7076 (mtp-110) REVERT: B 197 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.6982 (mtp180) REVERT: B 214 ARG cc_start: 0.7272 (mpt-90) cc_final: 0.6925 (mpt-90) REVERT: B 217 MET cc_start: 0.7731 (ptm) cc_final: 0.7474 (ptm) REVERT: B 219 ARG cc_start: 0.7839 (mtt-85) cc_final: 0.7606 (mmm-85) REVERT: B 335 PHE cc_start: 0.8655 (m-10) cc_final: 0.8250 (m-80) REVERT: R 65 MET cc_start: 0.6797 (tmm) cc_final: 0.5707 (tmm) REVERT: R 102 ARG cc_start: 0.8308 (ttp-170) cc_final: 0.8069 (ttp-170) REVERT: R 199 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7369 (ptt90) REVERT: R 326 MET cc_start: 0.6856 (mmm) cc_final: 0.6502 (mmm) outliers start: 29 outliers final: 24 residues processed: 182 average time/residue: 1.2974 time to fit residues: 250.7392 Evaluate side-chains 193 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 168 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 193 TRP Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.0040 chunk 93 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN B 220 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8528 Z= 0.169 Angle : 0.491 7.792 11559 Z= 0.256 Chirality : 0.040 0.139 1315 Planarity : 0.004 0.043 1458 Dihedral : 5.179 55.374 1277 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.20 % Allowed : 17.42 % Favored : 79.38 % 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: 0.99 (0.26), residues: 1033 helix: 1.56 (0.27), residues: 398 sheet: 0.85 (0.35), residues: 210 loop : -0.23 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.020 0.001 PHE R 87 TYR 0.020 0.001 TYR N 60 ARG 0.013 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.029 Fit side-chains REVERT: A 29 GLN cc_start: 0.7953 (tp40) cc_final: 0.7637 (mm-40) REVERT: A 33 ASP cc_start: 0.7085 (p0) cc_final: 0.6794 (p0) REVERT: A 39 ARG cc_start: 0.7558 (mtm110) cc_final: 0.7292 (ttp-110) REVERT: A 272 ASP cc_start: 0.7118 (m-30) cc_final: 0.6765 (m-30) REVERT: B 214 ARG cc_start: 0.7255 (mpt-90) cc_final: 0.6773 (mpp80) REVERT: B 217 MET cc_start: 0.7729 (ptm) cc_final: 0.7478 (ptm) REVERT: B 219 ARG cc_start: 0.7834 (mtt-85) cc_final: 0.7606 (mmm-85) REVERT: B 304 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7689 (ttp-170) REVERT: B 335 PHE cc_start: 0.8641 (m-10) cc_final: 0.8222 (m-80) REVERT: R 65 MET cc_start: 0.6769 (tmm) cc_final: 0.5664 (tmm) REVERT: R 199 ARG cc_start: 0.7751 (OUTLIER) cc_final: 0.7453 (ptt90) REVERT: R 326 MET cc_start: 0.6834 (mmm) cc_final: 0.6505 (mmm) outliers start: 29 outliers final: 24 residues processed: 181 average time/residue: 1.3857 time to fit residues: 265.1484 Evaluate side-chains 196 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 180 VAL Chi-restraints excluded: chain R residue 193 TRP Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 92 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 8 optimal weight: 0.3980 chunk 61 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN R 324 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8528 Z= 0.188 Angle : 0.488 7.886 11559 Z= 0.256 Chirality : 0.041 0.142 1315 Planarity : 0.004 0.044 1458 Dihedral : 5.173 56.590 1277 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.20 % Allowed : 17.42 % Favored : 79.38 % 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: 1.00 (0.26), residues: 1033 helix: 1.54 (0.27), residues: 394 sheet: 0.84 (0.34), residues: 215 loop : -0.18 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.021 0.001 PHE R 87 TYR 0.020 0.001 TYR N 60 ARG 0.007 0.000 ARG A 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.7958 (tp40) cc_final: 0.7648 (mm-40) REVERT: A 33 ASP cc_start: 0.7095 (p0) cc_final: 0.6799 (p0) REVERT: A 39 ARG cc_start: 0.7556 (mtm110) cc_final: 0.7291 (ttp-110) REVERT: A 272 ASP cc_start: 0.7128 (m-30) cc_final: 0.6762 (m-30) REVERT: B 217 MET cc_start: 0.7706 (ptm) cc_final: 0.7424 (ptm) REVERT: B 219 ARG cc_start: 0.7829 (mtt-85) cc_final: 0.7596 (mmm-85) REVERT: B 304 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7705 (ttp-170) REVERT: B 335 PHE cc_start: 0.8646 (m-10) cc_final: 0.8216 (m-80) REVERT: R 65 MET cc_start: 0.6709 (tmm) cc_final: 0.5571 (tmm) REVERT: R 199 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7480 (ptt90) REVERT: R 326 MET cc_start: 0.6835 (mmm) cc_final: 0.6516 (mmm) outliers start: 29 outliers final: 22 residues processed: 182 average time/residue: 1.3247 time to fit residues: 255.2499 Evaluate side-chains 191 residues out of total 907 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 167 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 347 ASP Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain R residue 47 THR Chi-restraints excluded: chain R residue 116 CYS Chi-restraints excluded: chain R residue 119 PHE Chi-restraints excluded: chain R residue 122 VAL Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 193 TRP Chi-restraints excluded: chain R residue 199 ARG Chi-restraints excluded: chain R residue 308 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN B 268 ASN C 12 GLN R 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.134287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.117483 restraints weight = 11356.067| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.02 r_work: 0.3413 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 8528 Z= 0.267 Angle : 0.531 8.245 11559 Z= 0.278 Chirality : 0.042 0.145 1315 Planarity : 0.004 0.044 1458 Dihedral : 5.373 57.669 1277 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.98 % Allowed : 18.19 % Favored : 78.83 % 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: 0.84 (0.26), residues: 1033 helix: 1.36 (0.26), residues: 399 sheet: 0.73 (0.34), residues: 223 loop : -0.26 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.007 0.001 HIS A 357 PHE 0.021 0.002 PHE R 87 TYR 0.020 0.002 TYR N 60 ARG 0.009 0.001 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4188.59 seconds wall clock time: 74 minutes 48.85 seconds (4488.85 seconds total)