Starting phenix.real_space_refine on Fri Jul 19 06:49:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/07_2024/9bkk_44643_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/07_2024/9bkk_44643.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/07_2024/9bkk_44643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/07_2024/9bkk_44643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/07_2024/9bkk_44643_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/07_2024/9bkk_44643_neut.cif" } resolution = 2.51 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= 0.100 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 56 5.16 5 C 4362 2.51 5 N 1156 2.21 5 O 1235 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 31": "NH1" <-> "NH2" Residue "A ARG 38": "NH1" <-> "NH2" Residue "A ARG 39": "NH1" <-> "NH2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 280": "NH1" <-> "NH2" Residue "A ARG 283": "NH1" <-> "NH2" Residue "A ARG 336": "NH1" <-> "NH2" Residue "A ARG 342": "NH1" <-> "NH2" Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 49": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 68": "NH1" <-> "NH2" Residue "B ARG 150": "NH1" <-> "NH2" Residue "B PHE 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 219": "NH1" <-> "NH2" Residue "B ARG 251": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 283": "NH1" <-> "NH2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G ARG 27": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 139": "NH1" <-> "NH2" Residue "R ARG 150": "NH1" <-> "NH2" Residue "R ARG 197": "NH1" <-> "NH2" Residue "R PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R ARG 313": "NH1" <-> "NH2" Residue "R ARG 336": "NH1" <-> "NH2" Residue "R ARG 345": "NH1" <-> "NH2" Residue "R ARG 346": "NH1" <-> "NH2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 378": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6809 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1599 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 3, 'TRANS': 199} Chain breaks: 4 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2497 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 3, 'ASP:plan': 4, 'ASN%COO:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 92 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 407 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 77 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 77 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TYS:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 2228 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2228 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 13, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 24 Time building chain proxies: 4.44, per 1000 atoms: 0.65 Number of scatterers: 6809 At special positions: 0 Unit cell: (84.15, 90.1, 126.65, 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 56 16.00 O 1235 8.00 N 1156 7.00 C 4362 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 114 " - pdb=" SG CYS R 196 " distance=2.05 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: 2.85 Conformation dependent library (CDL) restraints added in 1.2 seconds 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 9 sheets defined 47.8% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.569A pdb=" N ASN A 29 " --> pdb=" O MET A 25 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 36 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 293 through 303 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.905A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 352 removed outlier: 3.666A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.742A pdb=" N ARG A 389 " --> pdb=" O GLN A 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 7 through 25 removed outlier: 3.531A pdb=" N ILE G 25 " --> pdb=" O MET G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 39 through 69 Processing helix chain 'R' and resid 74 through 105 Proline residue: R 96 - end of helix Proline residue: R 101 - end of helix Processing helix chain 'R' and resid 110 through 145 removed outlier: 3.575A pdb=" N VAL R 133 " --> pdb=" O THR R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 152 Processing helix chain 'R' and resid 154 through 173 Processing helix chain 'R' and resid 174 through 179 removed outlier: 3.762A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 202 through 217 Processing helix chain 'R' and resid 218 through 238 removed outlier: 3.828A pdb=" N MET R 225 " --> pdb=" O PRO R 221 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR R 229 " --> pdb=" O MET R 225 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 348 removed outlier: 3.671A pdb=" N MET R 314 " --> pdb=" O ARG R 310 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE R 323 " --> pdb=" O VAL R 319 " (cutoff:3.500A) Proline residue: R 328 - end of helix removed outlier: 8.237A pdb=" N ALA R 341 " --> pdb=" O ALA R 337 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N SER R 342 " --> pdb=" O TYR R 338 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 371 removed outlier: 3.877A pdb=" N SER R 353 " --> pdb=" O GLY R 349 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N PHE R 354 " --> pdb=" O THR R 350 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N SER R 363 " --> pdb=" O SER R 359 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N CYS R 364 " --> pdb=" O TYR R 360 " (cutoff:3.500A) Proline residue: R 367 - end of helix Processing helix chain 'R' and resid 374 through 385 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 9.749A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASP A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.595A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.598A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.900A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.659A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.521A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.370A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.816A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'R' and resid 183 through 186 400 hydrogen bonds defined for protein. 1152 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: 2.05 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1198 1.32 - 1.44: 1778 1.44 - 1.57: 3886 1.57 - 1.69: 1 1.69 - 1.82: 82 Bond restraints: 6945 Sorted by residual: bond pdb=" C MET R 327 " pdb=" O MET R 327 " ideal model delta sigma weight residual 1.241 1.194 0.047 9.80e-03 1.04e+04 2.29e+01 bond pdb=" OH TYS P 2 " pdb=" S TYS P 2 " ideal model delta sigma weight residual 1.679 1.595 0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" N VAL B 158 " pdb=" CA VAL B 158 " ideal model delta sigma weight residual 1.459 1.511 -0.052 1.26e-02 6.30e+03 1.69e+01 bond pdb=" N VAL R 183 " pdb=" CA VAL R 183 " ideal model delta sigma weight residual 1.457 1.494 -0.037 9.00e-03 1.23e+04 1.66e+01 bond pdb=" N ILE B 157 " pdb=" CA ILE B 157 " ideal model delta sigma weight residual 1.459 1.502 -0.043 1.19e-02 7.06e+03 1.33e+01 ... (remaining 6940 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.70: 159 105.70 - 113.02: 3411 113.02 - 120.35: 3343 120.35 - 127.67: 2475 127.67 - 135.00: 52 Bond angle restraints: 9440 Sorted by residual: angle pdb=" CA ASP A 347 " pdb=" CB ASP A 347 " pdb=" CG ASP A 347 " ideal model delta sigma weight residual 112.60 120.10 -7.50 1.00e+00 1.00e+00 5.63e+01 angle pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " pdb=" CG PHE B 151 " ideal model delta sigma weight residual 113.80 120.73 -6.93 1.00e+00 1.00e+00 4.80e+01 angle pdb=" N LEU B 152 " pdb=" CA LEU B 152 " pdb=" C LEU B 152 " ideal model delta sigma weight residual 113.12 104.89 8.23 1.25e+00 6.40e-01 4.34e+01 angle pdb=" N LYS B 301 " pdb=" CA LYS B 301 " pdb=" C LYS B 301 " ideal model delta sigma weight residual 113.72 105.47 8.25 1.30e+00 5.92e-01 4.03e+01 angle pdb=" CA PHE B 292 " pdb=" CB PHE B 292 " pdb=" CG PHE B 292 " ideal model delta sigma weight residual 113.80 119.76 -5.96 1.00e+00 1.00e+00 3.55e+01 ... (remaining 9435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.83: 3696 13.83 - 27.66: 314 27.66 - 41.48: 66 41.48 - 55.31: 20 55.31 - 69.14: 13 Dihedral angle restraints: 4109 sinusoidal: 1506 harmonic: 2603 Sorted by residual: dihedral pdb=" C ASP A 347 " pdb=" N ASP A 347 " pdb=" CA ASP A 347 " pdb=" CB ASP A 347 " ideal model delta harmonic sigma weight residual -122.60 -137.47 14.87 0 2.50e+00 1.60e-01 3.54e+01 dihedral pdb=" CA TRP B 332 " pdb=" C TRP B 332 " pdb=" N ASP B 333 " pdb=" CA ASP B 333 " ideal model delta harmonic sigma weight residual 180.00 150.30 29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" C LYS A 293 " pdb=" N LYS A 293 " pdb=" CA LYS A 293 " pdb=" CB LYS A 293 " ideal model delta harmonic sigma weight residual -122.60 -136.92 14.32 0 2.50e+00 1.60e-01 3.28e+01 ... (remaining 4106 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 808 0.101 - 0.202: 270 0.202 - 0.303: 24 0.303 - 0.404: 7 0.404 - 0.505: 3 Chirality restraints: 1112 Sorted by residual: chirality pdb=" CA ASP A 347 " pdb=" N ASP A 347 " pdb=" C ASP A 347 " pdb=" CB ASP A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.37e+00 chirality pdb=" CB THR B 321 " pdb=" CA THR B 321 " pdb=" OG1 THR B 321 " pdb=" CG2 THR B 321 " both_signs ideal model delta sigma weight residual False 2.55 2.05 0.50 2.00e-01 2.50e+01 6.33e+00 chirality pdb=" CA LYS A 293 " pdb=" N LYS A 293 " pdb=" C LYS A 293 " pdb=" CB LYS A 293 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.70e+00 ... (remaining 1109 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 277 " -0.134 2.00e-02 2.50e+03 7.00e-02 1.23e+02 pdb=" CG TRP A 277 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 277 " 0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP A 277 " 0.069 2.00e-02 2.50e+03 pdb=" NE1 TRP A 277 " 0.041 2.00e-02 2.50e+03 pdb=" CE2 TRP A 277 " 0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP A 277 " 0.102 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 277 " -0.071 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 277 " 0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP A 277 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 332 " -0.093 2.00e-02 2.50e+03 4.97e-02 6.18e+01 pdb=" CG TRP B 332 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TRP B 332 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP B 332 " 0.047 2.00e-02 2.50e+03 pdb=" NE1 TRP B 332 " 0.030 2.00e-02 2.50e+03 pdb=" CE2 TRP B 332 " 0.011 2.00e-02 2.50e+03 pdb=" CE3 TRP B 332 " 0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 332 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 332 " 0.028 2.00e-02 2.50e+03 pdb=" CH2 TRP B 332 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.075 2.00e-02 2.50e+03 4.45e-02 4.95e+01 pdb=" CG TRP A 281 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " -0.066 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " -0.026 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " -0.059 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " 0.019 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.019 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " 0.057 2.00e-02 2.50e+03 ... (remaining 1180 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2442 2.89 - 3.39: 6643 3.39 - 3.90: 11499 3.90 - 4.40: 13396 4.40 - 4.90: 22504 Nonbonded interactions: 56484 Sorted by model distance: nonbonded pdb=" O TRP P 5 " pdb=" NH1 ARG R 336 " model vdw 2.388 2.520 nonbonded pdb=" O MET A 25 " pdb=" ND2 ASN A 29 " model vdw 2.430 2.520 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.431 2.440 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.456 2.440 nonbonded pdb=" O THR R 74 " pdb=" N ASN R 77 " model vdw 2.470 2.520 ... (remaining 56479 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: 0.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 22.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 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 : 0.012 0.084 6945 Z= 0.795 Angle : 1.754 8.564 9440 Z= 1.211 Chirality : 0.097 0.505 1112 Planarity : 0.012 0.100 1183 Dihedral : 12.285 69.136 2408 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.92 % Allowed : 4.49 % Favored : 94.59 % Rotamer: Outliers : 2.54 % Allowed : 5.07 % Favored : 92.39 % Cbeta Deviations : 0.24 % 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: -1.67 (0.26), residues: 868 helix: -1.29 (0.23), residues: 384 sheet: 1.39 (0.48), residues: 108 loop : -1.57 (0.30), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.134 0.019 TRP A 277 HIS 0.016 0.004 HIS B 225 PHE 0.052 0.008 PHE B 278 TYR 0.086 0.012 TYR R 176 ARG 0.007 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 186 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 36 LYS cc_start: 0.6626 (mtmm) cc_final: 0.6390 (mttt) REVERT: A 211 LYS cc_start: 0.7444 (mtpt) cc_final: 0.6752 (mttt) REVERT: A 280 ARG cc_start: 0.6407 (ttp-110) cc_final: 0.6043 (ttt-90) REVERT: A 338 LYS cc_start: 0.5288 (mtpt) cc_final: 0.5070 (mttt) REVERT: A 371 ASN cc_start: 0.6838 (m-40) cc_final: 0.6278 (m-40) REVERT: A 386 MET cc_start: 0.6013 (ttp) cc_final: 0.5640 (ptp) REVERT: B 59 TYR cc_start: 0.6551 (OUTLIER) cc_final: 0.6182 (m-80) REVERT: B 277 SER cc_start: 0.7346 (t) cc_final: 0.6991 (m) REVERT: R 69 ASN cc_start: 0.5960 (t0) cc_final: 0.5413 (m-40) REVERT: R 148 GLN cc_start: 0.6204 (mp10) cc_final: 0.5799 (mm-40) REVERT: R 160 LYS cc_start: 0.4549 (mmtp) cc_final: 0.4236 (tmtt) REVERT: R 194 ASN cc_start: 0.6196 (m-40) cc_final: 0.5955 (m-40) REVERT: R 217 LEU cc_start: 0.6623 (OUTLIER) cc_final: 0.6391 (tt) REVERT: R 225 MET cc_start: 0.7046 (mtp) cc_final: 0.6846 (mtm) REVERT: R 235 GLU cc_start: 0.5738 (mm-30) cc_final: 0.5183 (tt0) REVERT: R 310 ARG cc_start: 0.5341 (ttm-80) cc_final: 0.5069 (ptm-80) REVERT: R 344 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6559 (mt-10) REVERT: R 348 SER cc_start: 0.6946 (t) cc_final: 0.6497 (m) outliers start: 18 outliers final: 2 residues processed: 197 average time/residue: 1.0875 time to fit residues: 225.6661 Evaluate side-chains 125 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain R residue 217 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 267 GLN B 88 ASN B 259 GLN G 18 GLN R 333 ASN R 366 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6006 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6945 Z= 0.214 Angle : 0.646 9.997 9440 Z= 0.342 Chirality : 0.045 0.164 1112 Planarity : 0.005 0.066 1183 Dihedral : 6.255 69.912 957 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.80 % Allowed : 14.65 % Favored : 81.55 % 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: 0.53 (0.29), residues: 868 helix: 1.34 (0.26), residues: 387 sheet: 0.25 (0.37), residues: 196 loop : -0.87 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 169 HIS 0.006 0.002 HIS B 91 PHE 0.016 0.002 PHE B 151 TYR 0.015 0.002 TYR R 176 ARG 0.009 0.001 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7249 (mtpt) cc_final: 0.6731 (mmtt) REVERT: A 271 ASN cc_start: 0.4796 (m-40) cc_final: 0.4399 (m-40) REVERT: A 274 LYS cc_start: 0.5550 (tttt) cc_final: 0.5236 (ttmp) REVERT: A 280 ARG cc_start: 0.6332 (ttp-110) cc_final: 0.5921 (ttt-90) REVERT: A 343 LYS cc_start: 0.6600 (tmtt) cc_final: 0.6375 (tmmt) REVERT: A 371 ASN cc_start: 0.6973 (m-40) cc_final: 0.6562 (m-40) REVERT: A 386 MET cc_start: 0.5928 (ttp) cc_final: 0.5529 (ptp) REVERT: B 277 SER cc_start: 0.7541 (t) cc_final: 0.7267 (m) REVERT: R 69 ASN cc_start: 0.6441 (t0) cc_final: 0.5216 (m-40) REVERT: R 160 LYS cc_start: 0.4058 (mmtp) cc_final: 0.3840 (tmtt) REVERT: R 202 ASN cc_start: 0.5227 (p0) cc_final: 0.4549 (p0) outliers start: 27 outliers final: 9 residues processed: 145 average time/residue: 1.1530 time to fit residues: 176.1431 Evaluate side-chains 109 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 350 THR Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 78 optimal weight: 5.9990 chunk 84 optimal weight: 0.0470 chunk 69 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 254 ASN B 75 GLN G 18 GLN R 210 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6100 moved from start: 0.4087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6945 Z= 0.210 Angle : 0.606 9.893 9440 Z= 0.319 Chirality : 0.045 0.184 1112 Planarity : 0.004 0.052 1183 Dihedral : 5.546 72.140 952 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 4.37 % Allowed : 15.21 % Favored : 80.42 % 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: 0.95 (0.29), residues: 868 helix: 1.85 (0.26), residues: 384 sheet: 0.21 (0.37), residues: 189 loop : -0.66 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 169 HIS 0.006 0.002 HIS B 225 PHE 0.014 0.002 PHE B 199 TYR 0.019 0.002 TYR R 176 ARG 0.006 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 113 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7183 (mtpt) cc_final: 0.6725 (mmtt) REVERT: A 271 ASN cc_start: 0.4813 (m-40) cc_final: 0.4234 (m-40) REVERT: A 274 LYS cc_start: 0.5629 (tttt) cc_final: 0.5287 (ttmp) REVERT: A 280 ARG cc_start: 0.6459 (ttp-110) cc_final: 0.6131 (ttp80) REVERT: A 343 LYS cc_start: 0.6785 (tmtt) cc_final: 0.6370 (ttpt) REVERT: A 371 ASN cc_start: 0.6909 (m-40) cc_final: 0.6555 (m-40) REVERT: A 386 MET cc_start: 0.6021 (ttp) cc_final: 0.5622 (ptp) REVERT: B 226 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.5700 (mp0) REVERT: B 277 SER cc_start: 0.7708 (t) cc_final: 0.7385 (m) REVERT: R 45 ILE cc_start: 0.5704 (pt) cc_final: 0.5289 (mt) REVERT: R 160 LYS cc_start: 0.4270 (mmtp) cc_final: 0.3988 (tmtt) REVERT: R 223 VAL cc_start: 0.5024 (t) cc_final: 0.4783 (t) REVERT: R 233 SER cc_start: 0.6132 (OUTLIER) cc_final: 0.5725 (m) REVERT: R 235 GLU cc_start: 0.5727 (mm-30) cc_final: 0.5103 (tt0) REVERT: R 306 MET cc_start: 0.3393 (OUTLIER) cc_final: 0.3188 (mmt) outliers start: 31 outliers final: 12 residues processed: 133 average time/residue: 1.1292 time to fit residues: 158.2466 Evaluate side-chains 117 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 102 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 361 THR Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 83 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 0.1980 chunk 22 optimal weight: 5.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 254 ASN R 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6098 moved from start: 0.4475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6945 Z= 0.173 Angle : 0.531 6.150 9440 Z= 0.281 Chirality : 0.042 0.134 1112 Planarity : 0.004 0.045 1183 Dihedral : 5.260 71.378 952 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 3.80 % Allowed : 16.48 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.28), residues: 868 helix: 2.21 (0.26), residues: 381 sheet: 0.22 (0.36), residues: 188 loop : -0.59 (0.35), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.012 0.002 PHE B 199 TYR 0.018 0.001 TYR R 179 ARG 0.006 0.001 ARG R 378 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.723 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7212 (mtpt) cc_final: 0.6787 (mmtt) REVERT: A 271 ASN cc_start: 0.4748 (m-40) cc_final: 0.4121 (m-40) REVERT: A 274 LYS cc_start: 0.5766 (tttt) cc_final: 0.5431 (ttmp) REVERT: A 343 LYS cc_start: 0.6915 (tmtt) cc_final: 0.6558 (tmmt) REVERT: A 371 ASN cc_start: 0.6939 (m-40) cc_final: 0.6580 (m-40) REVERT: A 386 MET cc_start: 0.5951 (ttp) cc_final: 0.5496 (ptm) REVERT: B 19 ARG cc_start: 0.8016 (mmm160) cc_final: 0.7577 (mtp-110) REVERT: B 226 GLU cc_start: 0.7173 (OUTLIER) cc_final: 0.5698 (mp0) REVERT: B 277 SER cc_start: 0.7689 (t) cc_final: 0.7366 (m) REVERT: G 19 LEU cc_start: 0.6223 (OUTLIER) cc_final: 0.5911 (mm) REVERT: R 45 ILE cc_start: 0.5733 (pt) cc_final: 0.5349 (mt) REVERT: R 129 THR cc_start: 0.5828 (OUTLIER) cc_final: 0.5580 (m) REVERT: R 148 GLN cc_start: 0.6395 (OUTLIER) cc_final: 0.5907 (mm-40) REVERT: R 223 VAL cc_start: 0.4992 (t) cc_final: 0.4742 (t) REVERT: R 235 GLU cc_start: 0.5699 (mm-30) cc_final: 0.5191 (tt0) REVERT: R 306 MET cc_start: 0.3400 (OUTLIER) cc_final: 0.3199 (mmt) REVERT: R 346 ARG cc_start: 0.6073 (mmt180) cc_final: 0.5611 (tpm170) outliers start: 27 outliers final: 11 residues processed: 123 average time/residue: 1.1886 time to fit residues: 154.0095 Evaluate side-chains 112 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 148 GLN Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 350 THR Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.3980 chunk 47 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 74 optimal weight: 0.0670 chunk 20 optimal weight: 1.9990 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 254 ASN R 131 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 moved from start: 0.4795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6945 Z= 0.178 Angle : 0.538 5.779 9440 Z= 0.283 Chirality : 0.042 0.132 1112 Planarity : 0.004 0.041 1183 Dihedral : 5.254 72.093 952 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.94 % Allowed : 17.32 % Favored : 78.73 % 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: 1.30 (0.28), residues: 868 helix: 2.17 (0.26), residues: 388 sheet: 0.22 (0.36), residues: 189 loop : -0.43 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.013 0.002 PHE B 151 TYR 0.019 0.001 TYR R 179 ARG 0.005 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7242 (mtpt) cc_final: 0.6848 (mmtt) REVERT: A 271 ASN cc_start: 0.4798 (m-40) cc_final: 0.4166 (m-40) REVERT: A 274 LYS cc_start: 0.5744 (tttt) cc_final: 0.5393 (ttmp) REVERT: A 314 GLU cc_start: 0.5701 (mt-10) cc_final: 0.5055 (mp0) REVERT: A 336 ARG cc_start: 0.5533 (OUTLIER) cc_final: 0.5305 (ttt180) REVERT: A 343 LYS cc_start: 0.6965 (tmtt) cc_final: 0.6591 (tmmt) REVERT: A 371 ASN cc_start: 0.6897 (m-40) cc_final: 0.6539 (m-40) REVERT: A 386 MET cc_start: 0.5977 (ttp) cc_final: 0.5515 (ptm) REVERT: B 226 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.5702 (mp0) REVERT: B 277 SER cc_start: 0.7706 (t) cc_final: 0.7369 (m) REVERT: R 45 ILE cc_start: 0.5580 (pt) cc_final: 0.5256 (mt) REVERT: R 129 THR cc_start: 0.5752 (OUTLIER) cc_final: 0.5521 (m) REVERT: R 148 GLN cc_start: 0.6374 (OUTLIER) cc_final: 0.5894 (mm-40) REVERT: R 223 VAL cc_start: 0.5043 (t) cc_final: 0.4780 (t) REVERT: R 235 GLU cc_start: 0.5807 (mm-30) cc_final: 0.5290 (tt0) REVERT: R 346 ARG cc_start: 0.6000 (mmt180) cc_final: 0.5535 (tpm170) outliers start: 28 outliers final: 9 residues processed: 117 average time/residue: 1.2958 time to fit residues: 159.6953 Evaluate side-chains 107 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 148 GLN Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 48 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 69 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6113 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6945 Z= 0.173 Angle : 0.542 6.554 9440 Z= 0.282 Chirality : 0.042 0.131 1112 Planarity : 0.004 0.040 1183 Dihedral : 5.228 71.617 952 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.94 % Allowed : 18.31 % Favored : 77.75 % 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 (0.28), residues: 868 helix: 2.31 (0.26), residues: 385 sheet: 0.33 (0.36), residues: 187 loop : -0.44 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.011 0.001 PHE B 151 TYR 0.020 0.001 TYR R 179 ARG 0.006 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7172 (mtpt) cc_final: 0.6770 (mmtp) REVERT: A 271 ASN cc_start: 0.4856 (m-40) cc_final: 0.4208 (m-40) REVERT: A 274 LYS cc_start: 0.5747 (tttt) cc_final: 0.5412 (ttmp) REVERT: A 314 GLU cc_start: 0.5744 (mt-10) cc_final: 0.5291 (mp0) REVERT: A 336 ARG cc_start: 0.5496 (OUTLIER) cc_final: 0.5288 (ttt180) REVERT: A 343 LYS cc_start: 0.7003 (tmtt) cc_final: 0.6672 (ttpt) REVERT: A 371 ASN cc_start: 0.6923 (m-40) cc_final: 0.6561 (m-40) REVERT: A 386 MET cc_start: 0.6021 (ttp) cc_final: 0.5447 (ptp) REVERT: B 19 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7612 (mtp-110) REVERT: B 215 GLU cc_start: 0.5983 (OUTLIER) cc_final: 0.5458 (mt-10) REVERT: B 217 MET cc_start: 0.6640 (OUTLIER) cc_final: 0.4956 (pmt) REVERT: B 219 ARG cc_start: 0.7429 (ttm170) cc_final: 0.7027 (mmt90) REVERT: B 226 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.5710 (mp0) REVERT: B 277 SER cc_start: 0.7700 (t) cc_final: 0.7351 (m) REVERT: G 19 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.6016 (mm) REVERT: R 45 ILE cc_start: 0.5581 (pt) cc_final: 0.5273 (mt) REVERT: R 129 THR cc_start: 0.5734 (OUTLIER) cc_final: 0.5469 (m) REVERT: R 223 VAL cc_start: 0.5014 (t) cc_final: 0.4752 (t) REVERT: R 235 GLU cc_start: 0.5907 (mm-30) cc_final: 0.5223 (mt-10) REVERT: R 338 TYR cc_start: 0.7016 (m-80) cc_final: 0.6665 (m-80) REVERT: R 346 ARG cc_start: 0.5999 (mmt180) cc_final: 0.5561 (tpm170) REVERT: R 376 ARG cc_start: 0.7037 (ttm170) cc_final: 0.6689 (mtm-85) outliers start: 28 outliers final: 11 residues processed: 129 average time/residue: 1.0671 time to fit residues: 145.3303 Evaluate side-chains 118 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 46 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.3980 chunk 50 optimal weight: 0.2980 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 254 ASN ** R 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6143 moved from start: 0.5125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6945 Z= 0.219 Angle : 0.574 7.507 9440 Z= 0.301 Chirality : 0.043 0.180 1112 Planarity : 0.004 0.040 1183 Dihedral : 5.441 74.315 952 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 4.08 % Allowed : 18.59 % Favored : 77.32 % 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 (0.28), residues: 868 helix: 2.12 (0.26), residues: 385 sheet: 0.17 (0.36), residues: 186 loop : -0.52 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.009 0.001 HIS A 220 PHE 0.015 0.002 PHE B 151 TYR 0.014 0.002 TYR R 176 ARG 0.005 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 103 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7067 (mtpt) cc_final: 0.6770 (mmtp) REVERT: A 271 ASN cc_start: 0.4856 (m-40) cc_final: 0.4251 (m-40) REVERT: A 274 LYS cc_start: 0.5721 (tttt) cc_final: 0.5386 (ttmt) REVERT: A 314 GLU cc_start: 0.5711 (mt-10) cc_final: 0.5091 (mp0) REVERT: A 336 ARG cc_start: 0.5491 (OUTLIER) cc_final: 0.5253 (ttt180) REVERT: A 343 LYS cc_start: 0.7025 (tmtt) cc_final: 0.6699 (ttpt) REVERT: A 371 ASN cc_start: 0.6759 (m-40) cc_final: 0.6398 (m-40) REVERT: A 386 MET cc_start: 0.6053 (ttp) cc_final: 0.5417 (ptp) REVERT: B 19 ARG cc_start: 0.8040 (mmm160) cc_final: 0.7583 (mtp-110) REVERT: B 215 GLU cc_start: 0.5930 (OUTLIER) cc_final: 0.5621 (mt-10) REVERT: B 226 GLU cc_start: 0.7238 (OUTLIER) cc_final: 0.5760 (mp0) REVERT: B 277 SER cc_start: 0.7770 (t) cc_final: 0.7427 (m) REVERT: G 19 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6135 (mm) REVERT: R 45 ILE cc_start: 0.5522 (pt) cc_final: 0.5226 (mt) REVERT: R 148 GLN cc_start: 0.6379 (OUTLIER) cc_final: 0.5895 (mm-40) REVERT: R 223 VAL cc_start: 0.5133 (t) cc_final: 0.4881 (t) REVERT: R 235 GLU cc_start: 0.5910 (mm-30) cc_final: 0.5191 (mt-10) REVERT: R 338 TYR cc_start: 0.7036 (m-80) cc_final: 0.6696 (m-10) REVERT: R 346 ARG cc_start: 0.5999 (mmt180) cc_final: 0.5549 (tpm170) REVERT: R 369 ILE cc_start: 0.5981 (tt) cc_final: 0.5581 (pt) REVERT: R 376 ARG cc_start: 0.7052 (ttm170) cc_final: 0.6663 (mtm-85) outliers start: 29 outliers final: 14 residues processed: 122 average time/residue: 1.2187 time to fit residues: 156.8464 Evaluate side-chains 121 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 148 GLN Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 75 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** R 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6945 Z= 0.184 Angle : 0.553 7.758 9440 Z= 0.287 Chirality : 0.042 0.154 1112 Planarity : 0.004 0.039 1183 Dihedral : 5.384 74.507 952 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.10 % Allowed : 19.86 % Favored : 77.04 % 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: 1.22 (0.28), residues: 868 helix: 2.23 (0.26), residues: 385 sheet: 0.08 (0.35), residues: 188 loop : -0.57 (0.35), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.006 0.001 HIS A 220 PHE 0.019 0.002 PHE R 93 TYR 0.011 0.001 TYR R 338 ARG 0.006 0.001 ARG R 73 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.6967 (mtpt) cc_final: 0.6725 (mmtt) REVERT: A 271 ASN cc_start: 0.4848 (m-40) cc_final: 0.4232 (m-40) REVERT: A 274 LYS cc_start: 0.5691 (tttt) cc_final: 0.5359 (ttmt) REVERT: A 314 GLU cc_start: 0.5682 (mt-10) cc_final: 0.5104 (mp0) REVERT: A 336 ARG cc_start: 0.5482 (OUTLIER) cc_final: 0.5251 (ttt180) REVERT: A 343 LYS cc_start: 0.7021 (tmtt) cc_final: 0.6700 (ttpt) REVERT: A 371 ASN cc_start: 0.6744 (m-40) cc_final: 0.6378 (m-40) REVERT: A 386 MET cc_start: 0.6037 (ttp) cc_final: 0.5404 (ptp) REVERT: B 19 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7611 (mtp-110) REVERT: B 215 GLU cc_start: 0.5957 (OUTLIER) cc_final: 0.5444 (mt-10) REVERT: B 217 MET cc_start: 0.6716 (ptt) cc_final: 0.5180 (pmt) REVERT: B 226 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.5752 (mp0) REVERT: B 277 SER cc_start: 0.7764 (t) cc_final: 0.7415 (m) REVERT: G 19 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6164 (mm) REVERT: R 45 ILE cc_start: 0.5499 (pt) cc_final: 0.5229 (mt) REVERT: R 148 GLN cc_start: 0.6379 (OUTLIER) cc_final: 0.5899 (mm-40) REVERT: R 223 VAL cc_start: 0.5173 (t) cc_final: 0.4912 (t) REVERT: R 235 GLU cc_start: 0.5829 (mm-30) cc_final: 0.5215 (mt-10) REVERT: R 346 ARG cc_start: 0.5890 (mmt180) cc_final: 0.5472 (tpm170) REVERT: R 376 ARG cc_start: 0.7034 (ttm170) cc_final: 0.6677 (mtm-85) outliers start: 22 outliers final: 14 residues processed: 117 average time/residue: 1.2320 time to fit residues: 151.4865 Evaluate side-chains 119 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 100 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 215 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 148 GLN Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 60 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 254 ASN ** R 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6945 Z= 0.154 Angle : 0.531 8.656 9440 Z= 0.276 Chirality : 0.041 0.139 1112 Planarity : 0.004 0.040 1183 Dihedral : 5.245 73.212 952 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.24 % Allowed : 19.72 % Favored : 77.04 % 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: 1.36 (0.28), residues: 868 helix: 2.36 (0.26), residues: 384 sheet: 0.13 (0.36), residues: 187 loop : -0.51 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.014 0.001 PHE A 212 TYR 0.008 0.001 TYR A 360 ARG 0.008 0.001 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 103 time to evaluate : 0.796 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.6874 (mtpt) cc_final: 0.6668 (mmtt) REVERT: A 271 ASN cc_start: 0.4801 (m-40) cc_final: 0.4209 (m-40) REVERT: A 274 LYS cc_start: 0.5715 (tttt) cc_final: 0.5391 (ttmt) REVERT: A 314 GLU cc_start: 0.5649 (mt-10) cc_final: 0.5097 (mp0) REVERT: A 343 LYS cc_start: 0.6994 (tmtt) cc_final: 0.6678 (ttpt) REVERT: A 371 ASN cc_start: 0.6759 (m-40) cc_final: 0.6395 (m-40) REVERT: A 386 MET cc_start: 0.6033 (ttp) cc_final: 0.5383 (ptp) REVERT: B 19 ARG cc_start: 0.8051 (mmm160) cc_final: 0.7654 (mtp-110) REVERT: B 219 ARG cc_start: 0.7598 (ttm170) cc_final: 0.7176 (mmt90) REVERT: B 226 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.5728 (mp0) REVERT: B 255 LEU cc_start: 0.5905 (mt) cc_final: 0.5675 (mp) REVERT: B 277 SER cc_start: 0.7739 (t) cc_final: 0.7384 (m) REVERT: G 19 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6147 (mm) REVERT: R 45 ILE cc_start: 0.5555 (pt) cc_final: 0.5269 (mt) REVERT: R 148 GLN cc_start: 0.6343 (OUTLIER) cc_final: 0.5860 (mm-40) REVERT: R 223 VAL cc_start: 0.5166 (t) cc_final: 0.4904 (t) REVERT: R 235 GLU cc_start: 0.5792 (mm-30) cc_final: 0.5242 (mt-10) REVERT: R 346 ARG cc_start: 0.5873 (mmt180) cc_final: 0.5457 (tpm170) REVERT: R 376 ARG cc_start: 0.7064 (ttm170) cc_final: 0.6738 (mtm-85) outliers start: 23 outliers final: 11 residues processed: 118 average time/residue: 1.2047 time to fit residues: 149.8036 Evaluate side-chains 114 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 148 GLN Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 85 optimal weight: 0.1980 chunk 78 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS ** R 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6106 moved from start: 0.5382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6945 Z= 0.151 Angle : 0.526 7.532 9440 Z= 0.274 Chirality : 0.041 0.138 1112 Planarity : 0.004 0.040 1183 Dihedral : 5.179 71.948 952 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.25 % Allowed : 21.41 % Favored : 76.34 % 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 (0.29), residues: 868 helix: 2.46 (0.26), residues: 384 sheet: 0.11 (0.36), residues: 187 loop : -0.48 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.004 0.001 HIS A 220 PHE 0.017 0.001 PHE R 93 TYR 0.007 0.001 TYR A 360 ARG 0.008 0.000 ARG A 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1736 Ramachandran restraints generated. 868 Oldfield, 0 Emsley, 868 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 104 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 271 ASN cc_start: 0.4825 (m-40) cc_final: 0.4203 (m-40) REVERT: A 274 LYS cc_start: 0.5727 (tttt) cc_final: 0.5408 (ttmt) REVERT: A 314 GLU cc_start: 0.5646 (mt-10) cc_final: 0.5104 (mp0) REVERT: A 343 LYS cc_start: 0.6990 (tmtt) cc_final: 0.6677 (ttpt) REVERT: A 371 ASN cc_start: 0.6747 (m-40) cc_final: 0.6388 (m-40) REVERT: A 386 MET cc_start: 0.6037 (ttp) cc_final: 0.5390 (ptp) REVERT: B 19 ARG cc_start: 0.8049 (mmm160) cc_final: 0.7647 (mtp-110) REVERT: B 219 ARG cc_start: 0.7575 (ttm170) cc_final: 0.7142 (mmt90) REVERT: B 226 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.5661 (mp0) REVERT: B 277 SER cc_start: 0.7742 (t) cc_final: 0.7390 (m) REVERT: G 19 LEU cc_start: 0.6494 (OUTLIER) cc_final: 0.6145 (mm) REVERT: R 45 ILE cc_start: 0.5547 (pt) cc_final: 0.5265 (mt) REVERT: R 52 PHE cc_start: 0.4613 (t80) cc_final: 0.4006 (t80) REVERT: R 148 GLN cc_start: 0.6340 (OUTLIER) cc_final: 0.5861 (mm-40) REVERT: R 223 VAL cc_start: 0.5135 (t) cc_final: 0.4863 (t) REVERT: R 235 GLU cc_start: 0.5787 (mm-30) cc_final: 0.5224 (mt-10) REVERT: R 346 ARG cc_start: 0.5892 (mmt180) cc_final: 0.5456 (tpm170) REVERT: R 376 ARG cc_start: 0.7097 (ttm170) cc_final: 0.6798 (mtm-85) outliers start: 16 outliers final: 12 residues processed: 114 average time/residue: 1.1765 time to fit residues: 141.2963 Evaluate side-chains 114 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 148 GLN Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.199963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154622 restraints weight = 7052.265| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.08 r_work: 0.3860 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3733 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6945 Z= 0.205 Angle : 0.578 10.513 9440 Z= 0.297 Chirality : 0.043 0.133 1112 Planarity : 0.004 0.040 1183 Dihedral : 5.367 73.211 952 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.96 % Allowed : 20.85 % Favored : 76.20 % 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: 1.28 (0.28), residues: 868 helix: 2.28 (0.26), residues: 385 sheet: 0.17 (0.37), residues: 175 loop : -0.55 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.008 0.001 HIS A 220 PHE 0.014 0.002 PHE A 212 TYR 0.010 0.001 TYR A 391 ARG 0.008 0.001 ARG R 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.06 seconds wall clock time: 58 minutes 33.76 seconds (3513.76 seconds total)