Starting phenix.real_space_refine on Sat Aug 3 03:49:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/08_2024/9bkk_44643_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/08_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_44643/08_2024/9bkk_44643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/08_2024/9bkk_44643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/08_2024/9bkk_44643_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/08_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-5409/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: 4.45, 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: 2.83 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: 2.10 Time building geometry restraints manager: 3.11 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 3.120 nonbonded pdb=" O MET A 25 " pdb=" ND2 ASN A 29 " model vdw 2.430 3.120 nonbonded pdb=" OG SER B 147 " pdb=" OG SER B 160 " model vdw 2.431 3.040 nonbonded pdb=" OH TYR B 264 " pdb=" O ALA B 299 " model vdw 2.456 3.040 nonbonded pdb=" O THR R 74 " pdb=" N ASN R 77 " model vdw 2.470 3.120 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.890 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: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 22.360 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.090 ------------------------------------------------------------------------------- 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 : 0.782 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: 1.1091 time to fit residues: 230.2681 Evaluate side-chains 125 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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: 2.9990 chunk 65 optimal weight: 10.0000 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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: 0.6054 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6945 Z= 0.263 Angle : 0.702 10.703 9440 Z= 0.372 Chirality : 0.047 0.166 1112 Planarity : 0.005 0.068 1183 Dihedral : 6.433 72.795 957 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.94 % Allowed : 14.08 % Favored : 81.97 % 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: 0.40 (0.28), residues: 868 helix: 1.18 (0.26), residues: 388 sheet: 0.25 (0.38), residues: 186 loop : -0.87 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP B 169 HIS 0.007 0.003 HIS A 220 PHE 0.019 0.002 PHE B 292 TYR 0.022 0.002 TYR R 176 ARG 0.007 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 153 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 125 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7323 (mtpt) cc_final: 0.6763 (mmtt) REVERT: A 271 ASN cc_start: 0.4878 (m-40) cc_final: 0.4430 (m-40) REVERT: A 274 LYS cc_start: 0.5558 (tttt) cc_final: 0.5202 (ttmp) REVERT: A 280 ARG cc_start: 0.6427 (ttp-110) cc_final: 0.5913 (tmt90) REVERT: A 343 LYS cc_start: 0.6609 (tmtt) cc_final: 0.6373 (tmmt) REVERT: A 371 ASN cc_start: 0.7013 (m-40) cc_final: 0.6627 (m-40) REVERT: A 386 MET cc_start: 0.5951 (ttp) cc_final: 0.5531 (ptp) REVERT: B 277 SER cc_start: 0.7643 (t) cc_final: 0.7362 (m) REVERT: R 45 ILE cc_start: 0.5558 (pt) cc_final: 0.5160 (mt) REVERT: R 69 ASN cc_start: 0.6439 (t0) cc_final: 0.5330 (m-40) REVERT: R 160 LYS cc_start: 0.4047 (mmtp) cc_final: 0.3811 (tmtt) REVERT: R 202 ASN cc_start: 0.5101 (p0) cc_final: 0.4495 (p0) outliers start: 28 outliers final: 10 residues processed: 141 average time/residue: 1.1346 time to fit residues: 168.6367 Evaluate side-chains 107 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 394 VAL Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 267 ASP 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 359 SER 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: 1.9990 chunk 24 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 131 ASN R 210 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6073 moved from start: 0.3999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6945 Z= 0.174 Angle : 0.580 9.325 9440 Z= 0.309 Chirality : 0.044 0.286 1112 Planarity : 0.004 0.051 1183 Dihedral : 5.449 71.225 952 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.66 % Allowed : 15.92 % 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: 1.04 (0.29), residues: 868 helix: 1.89 (0.26), residues: 388 sheet: 0.20 (0.36), residues: 187 loop : -0.54 (0.36), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.007 0.002 HIS A 220 PHE 0.012 0.002 PHE B 151 TYR 0.012 0.001 TYR R 176 ARG 0.004 0.000 ARG A 283 *********************** 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 138 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 0.745 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7216 (mtpt) cc_final: 0.6766 (mmtt) REVERT: A 271 ASN cc_start: 0.4747 (m-40) cc_final: 0.4213 (m-40) REVERT: A 274 LYS cc_start: 0.5639 (tttt) cc_final: 0.5287 (ttmp) REVERT: A 280 ARG cc_start: 0.6471 (ttp-110) cc_final: 0.6127 (ttp80) REVERT: A 343 LYS cc_start: 0.6793 (tmtt) cc_final: 0.6524 (ttpt) REVERT: A 371 ASN cc_start: 0.7033 (m-40) cc_final: 0.6658 (m-40) REVERT: A 386 MET cc_start: 0.6036 (ttp) cc_final: 0.5649 (ptp) REVERT: B 277 SER cc_start: 0.7711 (t) cc_final: 0.7375 (m) REVERT: R 45 ILE cc_start: 0.5690 (pt) cc_final: 0.5291 (mt) REVERT: R 160 LYS cc_start: 0.4235 (mmtp) cc_final: 0.3981 (tmtt) REVERT: R 233 SER cc_start: 0.6102 (OUTLIER) cc_final: 0.5688 (m) REVERT: R 235 GLU cc_start: 0.5722 (mm-30) cc_final: 0.5115 (tt0) outliers start: 26 outliers final: 9 residues processed: 126 average time/residue: 1.2076 time to fit residues: 160.0429 Evaluate side-chains 107 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 97 time to evaluate : 0.658 ------------------------------------------------------------------------------- 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 R residue 114 CYS Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 233 SER Chi-restraints excluded: chain R residue 306 MET 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: 3.9990 chunk 58 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6163 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6945 Z= 0.277 Angle : 0.643 7.736 9440 Z= 0.339 Chirality : 0.045 0.147 1112 Planarity : 0.005 0.045 1183 Dihedral : 5.861 79.280 952 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.21 % Allowed : 16.20 % Favored : 78.59 % 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: 0.69 (0.28), residues: 868 helix: 1.62 (0.26), residues: 388 sheet: -0.02 (0.36), residues: 187 loop : -0.72 (0.35), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.007 0.002 HIS A 220 PHE 0.015 0.002 PHE B 151 TYR 0.018 0.002 TYR R 179 ARG 0.005 0.001 ARG R 73 *********************** 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 140 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 103 time to evaluate : 0.779 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7300 (mtpt) cc_final: 0.6795 (mmtt) REVERT: A 271 ASN cc_start: 0.4857 (m-40) cc_final: 0.4224 (m-40) REVERT: A 274 LYS cc_start: 0.5676 (tttt) cc_final: 0.5295 (ttmp) REVERT: A 280 ARG cc_start: 0.6614 (ttp-110) cc_final: 0.6196 (ttp80) REVERT: A 343 LYS cc_start: 0.6945 (tmtt) cc_final: 0.6668 (tttm) REVERT: A 371 ASN cc_start: 0.6815 (m-40) cc_final: 0.6457 (m-40) REVERT: A 386 MET cc_start: 0.6036 (ttp) cc_final: 0.5624 (ptp) REVERT: B 215 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5791 (mt-10) REVERT: B 226 GLU cc_start: 0.7149 (OUTLIER) cc_final: 0.5603 (mp0) REVERT: B 277 SER cc_start: 0.7761 (t) cc_final: 0.7432 (m) REVERT: G 19 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5922 (mm) REVERT: R 45 ILE cc_start: 0.5558 (pt) cc_final: 0.5260 (mt) REVERT: R 160 LYS cc_start: 0.4376 (mmtp) cc_final: 0.4155 (tmtt) REVERT: R 233 SER cc_start: 0.6253 (OUTLIER) cc_final: 0.5877 (m) REVERT: R 235 GLU cc_start: 0.5828 (mm-30) cc_final: 0.5345 (tt0) REVERT: R 306 MET cc_start: 0.3466 (OUTLIER) cc_final: 0.2994 (pp-130) REVERT: R 338 TYR cc_start: 0.6818 (m-80) cc_final: 0.6482 (m-10) REVERT: R 346 ARG cc_start: 0.6060 (OUTLIER) cc_final: 0.5537 (tpm170) outliers start: 37 outliers final: 13 residues processed: 130 average time/residue: 1.1497 time to fit residues: 157.3177 Evaluate side-chains 116 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 97 time to evaluate : 0.840 ------------------------------------------------------------------------------- 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 215 GLU Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 114 CYS Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 194 ASN 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 346 ARG 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 69 optimal weight: 0.5980 chunk 47 optimal weight: 0.0050 chunk 1 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 374 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6169 moved from start: 0.5022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6945 Z= 0.261 Angle : 0.617 7.404 9440 Z= 0.325 Chirality : 0.044 0.140 1112 Planarity : 0.004 0.042 1183 Dihedral : 5.800 80.212 952 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.51 % Allowed : 17.32 % Favored : 78.17 % 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: 0.72 (0.28), residues: 868 helix: 1.67 (0.26), residues: 388 sheet: -0.07 (0.36), residues: 190 loop : -0.72 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.006 0.002 HIS A 220 PHE 0.015 0.002 PHE B 241 TYR 0.018 0.002 TYR R 179 ARG 0.005 0.001 ARG B 19 *********************** 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 135 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 103 time to evaluate : 0.752 Fit side-chains revert: symmetry clash REVERT: A 211 LYS cc_start: 0.7277 (mtpt) cc_final: 0.6769 (mmtt) REVERT: A 213 GLN cc_start: 0.5070 (OUTLIER) cc_final: 0.4641 (tp40) REVERT: A 271 ASN cc_start: 0.4953 (m-40) cc_final: 0.4325 (m-40) REVERT: A 274 LYS cc_start: 0.5676 (tttt) cc_final: 0.5321 (ttmt) REVERT: A 280 ARG cc_start: 0.6644 (ttp-110) cc_final: 0.6035 (ttt90) REVERT: A 314 GLU cc_start: 0.5812 (mt-10) cc_final: 0.5001 (mp0) REVERT: A 343 LYS cc_start: 0.7005 (tmtt) cc_final: 0.6667 (ttpt) REVERT: A 371 ASN cc_start: 0.6875 (m-40) cc_final: 0.6507 (m-40) REVERT: A 386 MET cc_start: 0.6195 (ttp) cc_final: 0.5735 (ptp) REVERT: B 19 ARG cc_start: 0.8100 (mmm160) cc_final: 0.7590 (mtp-110) REVERT: B 42 ARG cc_start: 0.4758 (mmp-170) cc_final: 0.4535 (mmp-170) REVERT: B 219 ARG cc_start: 0.7427 (ttm170) cc_final: 0.6983 (mmt90) REVERT: B 277 SER cc_start: 0.7767 (t) cc_final: 0.7431 (m) REVERT: R 45 ILE cc_start: 0.5590 (pt) cc_final: 0.5361 (mt) REVERT: R 52 PHE cc_start: 0.4722 (t80) cc_final: 0.4148 (t80) REVERT: R 160 LYS cc_start: 0.4465 (mmtp) cc_final: 0.4248 (tmtt) REVERT: R 233 SER cc_start: 0.6110 (OUTLIER) cc_final: 0.5740 (m) REVERT: R 235 GLU cc_start: 0.5919 (mm-30) cc_final: 0.5251 (mt-10) REVERT: R 306 MET cc_start: 0.3459 (OUTLIER) cc_final: 0.3004 (pp-130) REVERT: R 338 TYR cc_start: 0.7177 (m-80) cc_final: 0.6810 (m-10) REVERT: R 346 ARG cc_start: 0.5874 (OUTLIER) cc_final: 0.5311 (tpm170) outliers start: 32 outliers final: 10 residues processed: 125 average time/residue: 1.2458 time to fit residues: 163.2896 Evaluate side-chains 109 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 213 GLN 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 234 PHE 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 346 ARG 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: 7.9990 chunk 74 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 48 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 38 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- 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: 0.6129 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6945 Z= 0.167 Angle : 0.540 5.949 9440 Z= 0.287 Chirality : 0.042 0.136 1112 Planarity : 0.004 0.041 1183 Dihedral : 5.469 77.596 952 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.80 % Allowed : 18.45 % 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: 1.19 (0.29), residues: 868 helix: 2.23 (0.26), residues: 385 sheet: 0.06 (0.36), residues: 188 loop : -0.63 (0.36), residues: 295 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 0.011 0.001 PHE B 241 TYR 0.011 0.001 TYR R 338 ARG 0.006 0.001 ARG R 73 *********************** 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 134 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 107 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6089 (OUTLIER) cc_final: 0.5629 (mt) REVERT: A 211 LYS cc_start: 0.7117 (mtpt) cc_final: 0.6622 (mmtt) REVERT: A 271 ASN cc_start: 0.4838 (m-40) cc_final: 0.4242 (m-40) REVERT: A 274 LYS cc_start: 0.5713 (tttt) cc_final: 0.5356 (ttmp) REVERT: A 280 ARG cc_start: 0.6608 (ttp-110) cc_final: 0.6132 (ttp80) REVERT: A 314 GLU cc_start: 0.5772 (mt-10) cc_final: 0.5043 (mp0) REVERT: A 343 LYS cc_start: 0.6996 (tmtt) cc_final: 0.6668 (ttpt) REVERT: A 371 ASN cc_start: 0.6798 (m-40) cc_final: 0.6444 (m-40) REVERT: A 386 MET cc_start: 0.6129 (ttp) cc_final: 0.5579 (ptm) REVERT: B 19 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7608 (mtp-110) REVERT: B 217 MET cc_start: 0.6652 (ptt) cc_final: 0.6252 (pmt) REVERT: B 219 ARG cc_start: 0.7386 (ttm170) cc_final: 0.6960 (mmt90) REVERT: B 226 GLU cc_start: 0.7117 (OUTLIER) cc_final: 0.5713 (mp0) REVERT: B 277 SER cc_start: 0.7799 (t) cc_final: 0.7442 (m) REVERT: R 45 ILE cc_start: 0.5593 (pt) cc_final: 0.5367 (mt) REVERT: R 52 PHE cc_start: 0.4676 (t80) cc_final: 0.4105 (t80) REVERT: R 93 PHE cc_start: 0.6340 (m-80) cc_final: 0.5926 (m-10) REVERT: R 235 GLU cc_start: 0.5943 (mm-30) cc_final: 0.5291 (mt-10) REVERT: R 338 TYR cc_start: 0.7062 (m-80) cc_final: 0.6735 (m-10) REVERT: R 346 ARG cc_start: 0.5929 (OUTLIER) cc_final: 0.5373 (tpm170) outliers start: 27 outliers final: 9 residues processed: 124 average time/residue: 1.2069 time to fit residues: 157.1196 Evaluate side-chains 110 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 210 THR 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 223 THR Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 72 MET Chi-restraints excluded: chain R residue 346 ARG 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: 0.9990 chunk 47 optimal weight: 0.8980 chunk 60 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 chunk 46 optimal weight: 0.0270 chunk 82 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.3980 chunk 38 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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: 0.6114 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 6945 Z= 0.155 Angle : 0.538 7.183 9440 Z= 0.285 Chirality : 0.041 0.139 1112 Planarity : 0.004 0.041 1183 Dihedral : 5.360 75.876 952 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.96 % Allowed : 19.58 % Favored : 77.46 % 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: 2.40 (0.26), residues: 384 sheet: 0.17 (0.36), residues: 186 loop : -0.60 (0.35), residues: 298 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 0.011 0.001 PHE A 212 TYR 0.018 0.001 TYR R 179 ARG 0.005 0.000 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 123 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 102 time to evaluate : 0.702 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5591 (mt) REVERT: A 211 LYS cc_start: 0.7027 (mtpt) cc_final: 0.6507 (mmtt) REVERT: A 271 ASN cc_start: 0.4824 (m-40) cc_final: 0.4210 (m-40) REVERT: A 274 LYS cc_start: 0.5748 (tttt) cc_final: 0.5399 (ttmt) REVERT: A 280 ARG cc_start: 0.6586 (ttp-110) cc_final: 0.6108 (ttp80) REVERT: A 314 GLU cc_start: 0.5783 (mt-10) cc_final: 0.5163 (mp0) REVERT: A 343 LYS cc_start: 0.6994 (tmtt) cc_final: 0.6668 (ttpt) REVERT: A 371 ASN cc_start: 0.6780 (m-40) cc_final: 0.6410 (m-40) REVERT: A 373 ARG cc_start: 0.5537 (OUTLIER) cc_final: 0.5254 (tpp-160) REVERT: A 386 MET cc_start: 0.6037 (ttp) cc_final: 0.5408 (ptp) REVERT: B 19 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7596 (mtp-110) REVERT: B 217 MET cc_start: 0.6662 (ptt) cc_final: 0.6271 (pmt) REVERT: B 219 ARG cc_start: 0.7404 (ttm170) cc_final: 0.6973 (mmt90) REVERT: B 226 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.5644 (mp0) REVERT: B 277 SER cc_start: 0.7796 (t) cc_final: 0.7440 (m) REVERT: R 45 ILE cc_start: 0.5529 (pt) cc_final: 0.5309 (mt) REVERT: R 52 PHE cc_start: 0.4665 (t80) cc_final: 0.4057 (t80) REVERT: R 73 ARG cc_start: 0.7383 (tpp80) cc_final: 0.7146 (tpp80) REVERT: R 93 PHE cc_start: 0.6323 (m-80) cc_final: 0.5901 (m-10) REVERT: R 235 GLU cc_start: 0.5955 (mm-30) cc_final: 0.5288 (mt-10) REVERT: R 338 TYR cc_start: 0.7106 (m-80) cc_final: 0.6790 (m-80) REVERT: R 346 ARG cc_start: 0.5923 (OUTLIER) cc_final: 0.5359 (tpm170) REVERT: R 376 ARG cc_start: 0.7064 (ttm170) cc_final: 0.6546 (mtm-85) outliers start: 21 outliers final: 12 residues processed: 116 average time/residue: 1.2541 time to fit residues: 152.8231 Evaluate side-chains 112 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 373 ARG 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 234 PHE Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 346 ARG 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: 0.0070 chunk 16 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 1.1002 ------------------------------------------------------------------------------- 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: 0.6130 moved from start: 0.5333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6945 Z= 0.183 Angle : 0.558 7.826 9440 Z= 0.293 Chirality : 0.042 0.135 1112 Planarity : 0.004 0.040 1183 Dihedral : 5.434 75.973 952 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.38 % Allowed : 19.30 % 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: 1.33 (0.28), residues: 868 helix: 2.33 (0.26), residues: 385 sheet: 0.18 (0.36), residues: 186 loop : -0.58 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.008 0.001 HIS A 220 PHE 0.013 0.001 PHE B 151 TYR 0.011 0.001 TYR R 338 ARG 0.006 0.000 ARG A 38 *********************** 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 123 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 99 time to evaluate : 0.676 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6156 (OUTLIER) cc_final: 0.5677 (mt) REVERT: A 211 LYS cc_start: 0.6958 (mtpt) cc_final: 0.6593 (mmtt) REVERT: A 271 ASN cc_start: 0.4786 (m-40) cc_final: 0.4182 (m-40) REVERT: A 274 LYS cc_start: 0.5769 (tttt) cc_final: 0.5426 (ttmt) REVERT: A 280 ARG cc_start: 0.6467 (ttp-110) cc_final: 0.6117 (ttp80) REVERT: A 314 GLU cc_start: 0.5753 (mt-10) cc_final: 0.5172 (mp0) REVERT: A 343 LYS cc_start: 0.6995 (tmtt) cc_final: 0.6675 (ttpt) REVERT: A 371 ASN cc_start: 0.6772 (m-40) cc_final: 0.6408 (m-40) REVERT: A 373 ARG cc_start: 0.5559 (OUTLIER) cc_final: 0.5298 (tpp-160) REVERT: A 386 MET cc_start: 0.6118 (ttp) cc_final: 0.5440 (ptp) REVERT: B 19 ARG cc_start: 0.8042 (mmm160) cc_final: 0.7579 (mtp-110) REVERT: B 217 MET cc_start: 0.6662 (ptt) cc_final: 0.6253 (pmt) REVERT: B 219 ARG cc_start: 0.7391 (ttm170) cc_final: 0.6973 (mmt90) REVERT: B 226 GLU cc_start: 0.7096 (OUTLIER) cc_final: 0.5667 (mp0) REVERT: B 277 SER cc_start: 0.7804 (t) cc_final: 0.7445 (m) REVERT: G 19 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.6027 (mm) REVERT: R 45 ILE cc_start: 0.5538 (pt) cc_final: 0.5329 (mt) REVERT: R 73 ARG cc_start: 0.7418 (tpp80) cc_final: 0.7191 (tpp80) REVERT: R 93 PHE cc_start: 0.6345 (m-80) cc_final: 0.5939 (m-10) REVERT: R 223 VAL cc_start: 0.5203 (t) cc_final: 0.4902 (t) REVERT: R 235 GLU cc_start: 0.5891 (mm-30) cc_final: 0.5260 (mt-10) REVERT: R 346 ARG cc_start: 0.5909 (OUTLIER) cc_final: 0.5337 (tpm170) REVERT: R 376 ARG cc_start: 0.7047 (ttm170) cc_final: 0.6735 (mtm180) outliers start: 24 outliers final: 15 residues processed: 115 average time/residue: 1.1926 time to fit residues: 144.5074 Evaluate side-chains 116 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 390 GLU 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 234 PHE Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain P residue 3 MET Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 346 ARG 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: 0.7980 chunk 46 optimal weight: 0.4980 chunk 33 optimal weight: 0.0070 chunk 60 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 73 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.2600 ------------------------------------------------------------------------------- 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: 0.6142 moved from start: 0.5438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6945 Z= 0.198 Angle : 0.566 6.694 9440 Z= 0.299 Chirality : 0.042 0.137 1112 Planarity : 0.004 0.039 1183 Dihedral : 5.516 75.677 952 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.38 % Allowed : 19.72 % Favored : 76.90 % 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: 2.27 (0.25), residues: 386 sheet: 0.06 (0.36), residues: 188 loop : -0.61 (0.35), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.023 0.002 PHE R 52 TYR 0.010 0.001 TYR R 176 ARG 0.006 0.001 ARG R 73 *********************** 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: 24 poor density : 102 time to evaluate : 0.733 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6117 (OUTLIER) cc_final: 0.5663 (mt) REVERT: A 211 LYS cc_start: 0.6983 (mtpt) cc_final: 0.6546 (mmtt) REVERT: A 271 ASN cc_start: 0.4882 (m-40) cc_final: 0.4266 (m-40) REVERT: A 274 LYS cc_start: 0.5730 (tttt) cc_final: 0.5391 (ttmt) REVERT: A 280 ARG cc_start: 0.6460 (ttp-110) cc_final: 0.6077 (ttp80) REVERT: A 314 GLU cc_start: 0.5729 (mt-10) cc_final: 0.5202 (mp0) REVERT: A 343 LYS cc_start: 0.6997 (tmtt) cc_final: 0.6685 (ttpt) REVERT: A 371 ASN cc_start: 0.6775 (m-40) cc_final: 0.6410 (m-40) REVERT: A 373 ARG cc_start: 0.5589 (OUTLIER) cc_final: 0.5286 (tpp-160) REVERT: A 386 MET cc_start: 0.6119 (ttp) cc_final: 0.5564 (ptm) REVERT: B 19 ARG cc_start: 0.8076 (mmm160) cc_final: 0.7619 (mtp-110) REVERT: B 217 MET cc_start: 0.6665 (ptt) cc_final: 0.6326 (pmt) REVERT: B 226 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.5687 (mp0) REVERT: B 277 SER cc_start: 0.7801 (t) cc_final: 0.7445 (m) REVERT: G 19 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6167 (mm) REVERT: R 45 ILE cc_start: 0.5598 (pt) cc_final: 0.5373 (mt) REVERT: R 73 ARG cc_start: 0.7411 (tpp80) cc_final: 0.7193 (tpp80) REVERT: R 93 PHE cc_start: 0.6392 (m-80) cc_final: 0.5868 (m-10) REVERT: R 235 GLU cc_start: 0.5896 (mm-30) cc_final: 0.5458 (mt-10) REVERT: R 346 ARG cc_start: 0.5747 (OUTLIER) cc_final: 0.5218 (tpm170) REVERT: R 376 ARG cc_start: 0.7051 (ttm170) cc_final: 0.6759 (mtm180) outliers start: 24 outliers final: 13 residues processed: 117 average time/residue: 1.2164 time to fit residues: 149.7617 Evaluate side-chains 116 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU 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 373 ARG Chi-restraints excluded: chain A residue 390 GLU 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 252 LEU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 346 ARG Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Chi-restraints excluded: chain R residue 374 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 52 optimal weight: 0.0060 chunk 41 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8998 ------------------------------------------------------------------------------- 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: 0.6124 moved from start: 0.5520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6945 Z= 0.171 Angle : 0.554 8.886 9440 Z= 0.291 Chirality : 0.042 0.240 1112 Planarity : 0.004 0.038 1183 Dihedral : 5.458 74.743 952 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.96 % Allowed : 20.14 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.28), residues: 868 helix: 2.38 (0.26), residues: 386 sheet: -0.04 (0.35), residues: 190 loop : -0.61 (0.35), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.012 0.001 HIS A 220 PHE 0.026 0.002 PHE R 52 TYR 0.009 0.001 TYR A 360 ARG 0.005 0.001 ARG R 73 ********************** 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: 21 poor density : 99 time to evaluate : 0.742 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6164 (OUTLIER) cc_final: 0.5664 (mt) REVERT: A 211 LYS cc_start: 0.6952 (mtpt) cc_final: 0.6630 (mmtt) REVERT: A 271 ASN cc_start: 0.4811 (m-40) cc_final: 0.4211 (m-40) REVERT: A 274 LYS cc_start: 0.5758 (tttt) cc_final: 0.5427 (ttmt) REVERT: A 280 ARG cc_start: 0.6467 (ttp-110) cc_final: 0.6067 (ttp80) REVERT: A 314 GLU cc_start: 0.5757 (mt-10) cc_final: 0.5248 (mp0) REVERT: A 343 LYS cc_start: 0.7087 (tmtt) cc_final: 0.6775 (ttpt) REVERT: A 371 ASN cc_start: 0.6744 (m-40) cc_final: 0.6375 (m-40) REVERT: A 373 ARG cc_start: 0.5557 (OUTLIER) cc_final: 0.5281 (tpp-160) REVERT: A 386 MET cc_start: 0.6096 (ttp) cc_final: 0.5434 (ptp) REVERT: B 19 ARG cc_start: 0.8069 (mmm160) cc_final: 0.7586 (mtp-110) REVERT: B 217 MET cc_start: 0.6749 (ptt) cc_final: 0.5007 (pmt) REVERT: B 219 ARG cc_start: 0.7631 (ttm170) cc_final: 0.7267 (mmt90) REVERT: B 226 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.5680 (mp0) REVERT: B 277 SER cc_start: 0.7799 (t) cc_final: 0.7436 (m) REVERT: G 19 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6168 (mm) REVERT: R 45 ILE cc_start: 0.5684 (pt) cc_final: 0.5468 (mt) REVERT: R 73 ARG cc_start: 0.7376 (tpp80) cc_final: 0.7162 (tpp80) REVERT: R 93 PHE cc_start: 0.6390 (m-80) cc_final: 0.5861 (m-10) REVERT: R 223 VAL cc_start: 0.5198 (t) cc_final: 0.4897 (t) REVERT: R 235 GLU cc_start: 0.5942 (mm-30) cc_final: 0.5362 (mt-10) REVERT: R 346 ARG cc_start: 0.5735 (OUTLIER) cc_final: 0.5216 (tpm170) REVERT: R 376 ARG cc_start: 0.7053 (ttm170) cc_final: 0.6744 (mtp180) outliers start: 21 outliers final: 12 residues processed: 113 average time/residue: 1.2442 time to fit residues: 147.7581 Evaluate side-chains 113 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 358 ILE Chi-restraints excluded: chain A residue 373 ARG Chi-restraints excluded: chain A residue 390 GLU 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 252 LEU Chi-restraints excluded: chain B residue 293 ASN Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 346 ARG Chi-restraints excluded: chain R residue 359 SER Chi-restraints excluded: chain R residue 362 SER Chi-restraints excluded: chain R residue 374 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 28 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 3 optimal weight: 0.0770 chunk 49 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.203099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.158967 restraints weight = 7122.236| |-----------------------------------------------------------------------------| r_work (start): 0.4027 rms_B_bonded: 2.08 r_work: 0.3911 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3786 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.5615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6945 Z= 0.147 Angle : 0.523 8.530 9440 Z= 0.276 Chirality : 0.041 0.142 1112 Planarity : 0.004 0.038 1183 Dihedral : 5.245 71.041 952 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 2.68 % Allowed : 20.99 % 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: 1.51 (0.29), residues: 868 helix: 2.61 (0.26), residues: 385 sheet: 0.01 (0.35), residues: 188 loop : -0.48 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.004 0.001 HIS A 220 PHE 0.026 0.001 PHE R 52 TYR 0.007 0.001 TYR A 360 ARG 0.006 0.000 ARG R 73 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3309.38 seconds wall clock time: 60 minutes 58.92 seconds (3658.92 seconds total)