Starting phenix.real_space_refine on Tue Jun 25 05:36:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/06_2024/9bkk_44643_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/06_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_44643/06_2024/9bkk_44643.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/06_2024/9bkk_44643.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/06_2024/9bkk_44643_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bkk_44643/06_2024/9bkk_44643_neut_updated.pdb" } 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-5370/modules/chem_data/mon_lib" Total number of atoms: 6809 Number of models: 1 Model: "" Number of chains: 5 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 78 Unusual residues: {'NH2': 1} Classifications: {'peptide': 8, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, '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: "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: 4.74, per 1000 atoms: 0.70 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=0, symmetry=0 Time building additional restraints: 2.77 Conformation dependent library (CDL) restraints added in 1.3 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... running ksdssp... Secondary structure from input PDB file: 24 helices and 9 sheets defined 43.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.85 Creating SS restraints... Processing helix chain 'A' and resid 19 through 38 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 53 through 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 266 through 277 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 351 removed outlier: 3.666A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 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 25 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 7 through 24 Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'R' and resid 39 through 68 Processing helix chain 'R' and resid 75 through 104 Proline residue: R 96 - end of helix Proline residue: R 101 - end of helix Processing helix chain 'R' and resid 111 through 144 removed outlier: 3.575A pdb=" N VAL R 133 " --> pdb=" O THR R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 148 through 151 Processing helix chain 'R' and resid 155 through 178 removed outlier: 3.914A pdb=" N THR R 174 " --> pdb=" O PHE R 170 " (cutoff:3.500A) Proline residue: R 175 - end of helix removed outlier: 3.762A pdb=" N ILE R 178 " --> pdb=" O THR R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 216 Processing helix chain 'R' and resid 219 through 237 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 338 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 Processing helix chain 'R' and resid 340 through 347 Processing helix chain 'R' and resid 350 through 370 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 375 through 384 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.122A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ASN A 218 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.892A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (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= C, 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= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.682A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (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= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.819A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (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= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.729A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) 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= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.473A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.527A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'R' and resid 183 through 186 343 hydrogen bonds defined for protein. 996 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: 2.37 Time building geometry restraints manager: 3.04 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: 1779 1.44 - 1.57: 3886 1.57 - 1.69: 1 1.69 - 1.82: 82 Bond restraints: 6946 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 6941 not shown) Histogram of bond angle deviations from ideal: 98.37 - 105.70: 159 105.70 - 113.02: 3411 113.02 - 120.35: 3345 120.35 - 127.67: 2475 127.67 - 135.00: 52 Bond angle restraints: 9442 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 9437 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: 1184 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 1181 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 2450 2.89 - 3.39: 6693 3.39 - 3.90: 11556 3.90 - 4.40: 13501 4.40 - 4.90: 22512 Nonbonded interactions: 56712 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 56707 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: 1.440 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: 3.900 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 23.920 Find NCS groups from input model: 0.210 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:12.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.400 ------------------------------------------------------------------------------- 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 6946 Z= 0.804 Angle : 1.754 8.564 9442 Z= 1.211 Chirality : 0.097 0.505 1112 Planarity : 0.012 0.100 1184 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 : 0.689 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: 1.1241 time to fit residues: 233.1060 Evaluate side-chains 125 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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: 0.5980 chunk 65 optimal weight: 7.9990 chunk 36 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 G 18 GLN G 44 HIS R 131 ASN R 333 ASN R 366 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6946 Z= 0.179 Angle : 0.617 9.611 9442 Z= 0.328 Chirality : 0.044 0.158 1112 Planarity : 0.005 0.068 1184 Dihedral : 6.269 67.919 957 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.52 % Allowed : 15.21 % Favored : 81.27 % 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: 0.60 (0.29), residues: 868 helix: 1.33 (0.27), residues: 383 sheet: 0.38 (0.38), residues: 190 loop : -0.75 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 169 HIS 0.009 0.002 HIS A 220 PHE 0.014 0.002 PHE B 292 TYR 0.013 0.001 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 159 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: A 210 THR cc_start: 0.7415 (p) cc_final: 0.7214 (t) REVERT: A 211 LYS cc_start: 0.7255 (mtpt) cc_final: 0.6739 (mmtt) REVERT: A 271 ASN cc_start: 0.4673 (m-40) cc_final: 0.4360 (m-40) REVERT: A 280 ARG cc_start: 0.6360 (ttp-110) cc_final: 0.6033 (ttt-90) REVERT: A 343 LYS cc_start: 0.6583 (tmtt) cc_final: 0.6371 (tmmt) REVERT: A 371 ASN cc_start: 0.6867 (m-40) cc_final: 0.6458 (m-40) REVERT: A 377 ASN cc_start: 0.6794 (m-40) cc_final: 0.6589 (m-40) REVERT: A 386 MET cc_start: 0.6009 (ttp) cc_final: 0.5600 (ptp) REVERT: B 59 TYR cc_start: 0.6373 (m-80) cc_final: 0.6021 (m-80) REVERT: B 277 SER cc_start: 0.7548 (t) cc_final: 0.7206 (m) REVERT: R 69 ASN cc_start: 0.6473 (t0) cc_final: 0.5710 (m-40) REVERT: R 160 LYS cc_start: 0.4097 (mmtp) cc_final: 0.3854 (tmtt) REVERT: R 202 ASN cc_start: 0.5609 (p0) cc_final: 0.4981 (p0) REVERT: R 217 LEU cc_start: 0.6343 (OUTLIER) cc_final: 0.6123 (tt) REVERT: R 344 GLU cc_start: 0.7038 (mt-10) cc_final: 0.6594 (mt-10) REVERT: R 348 SER cc_start: 0.7152 (t) cc_final: 0.6619 (m) outliers start: 25 outliers final: 9 residues processed: 150 average time/residue: 1.1245 time to fit residues: 177.8521 Evaluate side-chains 117 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 ASP 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 R residue 114 CYS Chi-restraints excluded: chain R residue 217 LEU 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: 1.9990 chunk 24 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 84 optimal weight: 0.4980 chunk 69 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- 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 259 GLN G 18 GLN R 210 HIS R 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6105 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6946 Z= 0.222 Angle : 0.622 9.993 9442 Z= 0.325 Chirality : 0.045 0.185 1112 Planarity : 0.004 0.052 1184 Dihedral : 5.865 72.083 954 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 4.65 % Allowed : 15.21 % Favored : 80.14 % 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: 0.93 (0.29), residues: 868 helix: 1.67 (0.26), residues: 383 sheet: 0.36 (0.39), residues: 180 loop : -0.51 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.006 0.002 HIS A 220 PHE 0.015 0.002 PHE B 199 TYR 0.022 0.002 TYR R 176 ARG 0.003 0.001 ARG A 342 *********************** 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 147 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 0.798 Fit side-chains REVERT: A 211 LYS cc_start: 0.7157 (mtpt) cc_final: 0.6753 (mmtt) REVERT: A 271 ASN cc_start: 0.4782 (m-40) cc_final: 0.4246 (m-40) REVERT: A 274 LYS cc_start: 0.5820 (tttt) cc_final: 0.5413 (ttmp) REVERT: A 280 ARG cc_start: 0.6525 (ttp-110) cc_final: 0.6211 (ttp80) REVERT: A 343 LYS cc_start: 0.6741 (tmtt) cc_final: 0.6474 (tmmt) REVERT: A 371 ASN cc_start: 0.6948 (m-40) cc_final: 0.6582 (m-40) REVERT: A 386 MET cc_start: 0.5981 (ttp) cc_final: 0.5567 (ptp) REVERT: B 59 TYR cc_start: 0.6377 (m-80) cc_final: 0.5996 (m-80) REVERT: B 226 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.5740 (mp0) REVERT: B 277 SER cc_start: 0.7738 (t) cc_final: 0.7393 (m) REVERT: G 19 LEU cc_start: 0.6234 (OUTLIER) cc_final: 0.5886 (mm) REVERT: R 45 ILE cc_start: 0.5683 (pt) cc_final: 0.5307 (mt) REVERT: R 69 ASN cc_start: 0.6672 (t0) cc_final: 0.5797 (m-40) REVERT: R 148 GLN cc_start: 0.6442 (OUTLIER) cc_final: 0.5998 (mm-40) REVERT: R 160 LYS cc_start: 0.4256 (mmtp) cc_final: 0.3983 (tmtt) REVERT: R 223 VAL cc_start: 0.5048 (t) cc_final: 0.4803 (t) REVERT: R 233 SER cc_start: 0.6276 (OUTLIER) cc_final: 0.5892 (m) REVERT: R 235 GLU cc_start: 0.5753 (mm-30) cc_final: 0.5191 (tt0) REVERT: R 376 ARG cc_start: 0.6770 (ttm-80) cc_final: 0.6541 (mtm-85) outliers start: 33 outliers final: 12 residues processed: 135 average time/residue: 1.2293 time to fit residues: 174.9000 Evaluate side-chains 118 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 148 GLN Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 233 SER 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: 0.7980 chunk 58 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 78 optimal weight: 0.0970 chunk 83 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 22 optimal weight: 10.0000 overall best weight: 2.3582 ------------------------------------------------------------------------------- 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: 0.6189 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6946 Z= 0.309 Angle : 0.661 8.463 9442 Z= 0.349 Chirality : 0.046 0.142 1112 Planarity : 0.005 0.046 1184 Dihedral : 6.123 82.641 952 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.65 % Allowed : 15.07 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.28), residues: 868 helix: 1.41 (0.26), residues: 381 sheet: 0.21 (0.40), residues: 166 loop : -0.63 (0.33), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.007 0.002 HIS A 220 PHE 0.015 0.002 PHE B 151 TYR 0.020 0.002 TYR R 176 ARG 0.005 0.001 ARG B 19 *********************** 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 135 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 102 time to evaluate : 0.776 Fit side-chains REVERT: A 43 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5837 (mt) REVERT: A 211 LYS cc_start: 0.7253 (mtpt) cc_final: 0.6705 (mmtt) REVERT: A 271 ASN cc_start: 0.4968 (m-40) cc_final: 0.4304 (m-40) REVERT: A 274 LYS cc_start: 0.5823 (tttt) cc_final: 0.5484 (ttmp) REVERT: A 280 ARG cc_start: 0.6731 (ttp-110) cc_final: 0.6499 (ttp80) REVERT: A 314 GLU cc_start: 0.5857 (mt-10) cc_final: 0.5197 (mp0) REVERT: A 343 LYS cc_start: 0.6988 (tmtt) cc_final: 0.6753 (tttm) REVERT: A 386 MET cc_start: 0.6168 (ttp) cc_final: 0.5694 (ptm) REVERT: B 19 ARG cc_start: 0.8077 (mmm160) cc_final: 0.7867 (mmm160) REVERT: B 59 TYR cc_start: 0.6618 (m-80) cc_final: 0.6090 (m-80) REVERT: B 226 GLU cc_start: 0.7207 (OUTLIER) cc_final: 0.5754 (mp0) REVERT: G 19 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6206 (mm) REVERT: R 45 ILE cc_start: 0.5627 (pt) cc_final: 0.5337 (mt) REVERT: R 69 ASN cc_start: 0.6923 (t0) cc_final: 0.5967 (m-40) REVERT: R 160 LYS cc_start: 0.4440 (mmtp) cc_final: 0.4223 (tmtt) REVERT: R 223 VAL cc_start: 0.5245 (t) cc_final: 0.5018 (t) REVERT: R 233 SER cc_start: 0.6303 (OUTLIER) cc_final: 0.5975 (m) REVERT: R 235 GLU cc_start: 0.5826 (mm-30) cc_final: 0.5337 (tt0) REVERT: R 338 TYR cc_start: 0.7029 (m-80) cc_final: 0.6635 (m-80) REVERT: R 346 ARG cc_start: 0.6186 (OUTLIER) cc_final: 0.5410 (tmt170) REVERT: R 376 ARG cc_start: 0.6952 (ttm-80) cc_final: 0.6702 (mtm-85) outliers start: 33 outliers final: 14 residues processed: 124 average time/residue: 1.3090 time to fit residues: 170.1998 Evaluate side-chains 115 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 0.756 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain B residue 267 ASP 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 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: 1.9990 chunk 47 optimal weight: 0.9990 chunk 1 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 57 optimal weight: 7.9990 chunk 0 optimal weight: 0.6980 chunk 42 optimal weight: 0.0470 chunk 74 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.9082 ------------------------------------------------------------------------------- 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: 0.6139 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6946 Z= 0.161 Angle : 0.535 5.702 9442 Z= 0.282 Chirality : 0.042 0.135 1112 Planarity : 0.004 0.042 1184 Dihedral : 5.532 79.171 952 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.94 % Allowed : 17.18 % Favored : 78.87 % 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: 1.06 (0.28), residues: 868 helix: 2.06 (0.26), residues: 374 sheet: 0.05 (0.37), residues: 178 loop : -0.50 (0.34), residues: 316 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 0.009 0.001 TYR A 391 ARG 0.005 0.000 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 135 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 107 time to evaluate : 0.715 Fit side-chains REVERT: A 211 LYS cc_start: 0.7333 (mtpt) cc_final: 0.6776 (mmtt) REVERT: A 271 ASN cc_start: 0.4899 (m-40) cc_final: 0.4270 (m-40) REVERT: A 274 LYS cc_start: 0.5800 (tttt) cc_final: 0.5491 (ttmp) REVERT: A 280 ARG cc_start: 0.6639 (ttp-110) cc_final: 0.6403 (ttp80) REVERT: A 314 GLU cc_start: 0.5815 (mt-10) cc_final: 0.5229 (mp0) REVERT: A 343 LYS cc_start: 0.6991 (tmtt) cc_final: 0.6658 (ttpt) REVERT: A 371 ASN cc_start: 0.7052 (m-40) cc_final: 0.6687 (m-40) REVERT: A 386 MET cc_start: 0.6167 (ttp) cc_final: 0.5622 (ptm) REVERT: B 19 ARG cc_start: 0.8062 (mmm160) cc_final: 0.7844 (mmm160) REVERT: B 59 TYR cc_start: 0.6598 (m-80) cc_final: 0.6180 (m-80) REVERT: B 219 ARG cc_start: 0.7360 (ttm170) cc_final: 0.7004 (mmt90) REVERT: B 226 GLU cc_start: 0.7212 (OUTLIER) cc_final: 0.5835 (mp0) REVERT: B 277 SER cc_start: 0.7815 (t) cc_final: 0.7415 (m) REVERT: B 314 ARG cc_start: 0.5726 (ttp-170) cc_final: 0.5466 (ttt180) REVERT: G 19 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6077 (mm) REVERT: R 45 ILE cc_start: 0.5596 (pt) cc_final: 0.5312 (mt) REVERT: R 235 GLU cc_start: 0.5833 (mm-30) cc_final: 0.5345 (tt0) REVERT: R 338 TYR cc_start: 0.7012 (m-80) cc_final: 0.6602 (m-80) REVERT: R 346 ARG cc_start: 0.6004 (OUTLIER) cc_final: 0.5286 (tmt170) REVERT: R 369 ILE cc_start: 0.6093 (tt) cc_final: 0.5664 (pt) REVERT: R 376 ARG cc_start: 0.6967 (ttm-80) cc_final: 0.6756 (mtm-85) outliers start: 28 outliers final: 11 residues processed: 121 average time/residue: 1.3693 time to fit residues: 173.4026 Evaluate side-chains 114 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.801 ------------------------------------------------------------------------------- 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 234 PHE Chi-restraints excluded: chain B residue 267 ASP 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 215 LEU Chi-restraints excluded: chain R residue 346 ARG 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: 4.9990 chunk 74 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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: 0.6162 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6946 Z= 0.205 Angle : 0.558 6.788 9442 Z= 0.294 Chirality : 0.043 0.146 1112 Planarity : 0.004 0.042 1184 Dihedral : 5.611 80.268 952 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.80 % Allowed : 18.03 % 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: 1.05 (0.28), residues: 868 helix: 2.04 (0.26), residues: 376 sheet: 0.05 (0.37), residues: 178 loop : -0.52 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.007 0.001 HIS A 220 PHE 0.016 0.002 PHE R 93 TYR 0.013 0.001 TYR R 338 ARG 0.005 0.000 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 130 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 103 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6362 (OUTLIER) cc_final: 0.5875 (mt) REVERT: A 211 LYS cc_start: 0.7248 (mtpt) cc_final: 0.6736 (mmtp) REVERT: A 271 ASN cc_start: 0.4934 (m-40) cc_final: 0.4280 (m-40) REVERT: A 274 LYS cc_start: 0.5799 (tttt) cc_final: 0.5463 (ttmp) REVERT: A 280 ARG cc_start: 0.6620 (ttp-110) cc_final: 0.5842 (tmt90) REVERT: A 314 GLU cc_start: 0.5760 (mt-10) cc_final: 0.5196 (mp0) REVERT: A 343 LYS cc_start: 0.7025 (tmtt) cc_final: 0.6690 (ttpt) REVERT: A 371 ASN cc_start: 0.6937 (m-40) cc_final: 0.6570 (m-40) REVERT: A 386 MET cc_start: 0.6161 (ttp) cc_final: 0.5588 (ptm) REVERT: B 19 ARG cc_start: 0.8081 (mmm160) cc_final: 0.7862 (mmm160) REVERT: B 59 TYR cc_start: 0.6639 (m-80) cc_final: 0.6174 (m-80) REVERT: B 226 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.5832 (mp0) REVERT: B 314 ARG cc_start: 0.5797 (ttp-170) cc_final: 0.5463 (ttp-170) REVERT: G 19 LEU cc_start: 0.6478 (OUTLIER) cc_final: 0.6140 (mm) REVERT: R 45 ILE cc_start: 0.5568 (pt) cc_final: 0.5334 (mt) REVERT: R 52 PHE cc_start: 0.4666 (t80) cc_final: 0.4055 (t80) REVERT: R 235 GLU cc_start: 0.5878 (mm-30) cc_final: 0.5175 (mt-10) REVERT: R 338 TYR cc_start: 0.7038 (m-80) cc_final: 0.6602 (m-80) REVERT: R 346 ARG cc_start: 0.5868 (OUTLIER) cc_final: 0.5171 (tmt170) REVERT: R 376 ARG cc_start: 0.7038 (ttm-80) cc_final: 0.6775 (mtm-85) outliers start: 27 outliers final: 13 residues processed: 118 average time/residue: 1.4408 time to fit residues: 177.8405 Evaluate side-chains 113 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.792 ------------------------------------------------------------------------------- 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 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 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 118 THR 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 346 ARG 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: 6.9990 chunk 47 optimal weight: 0.0670 chunk 60 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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: 0.6163 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6946 Z= 0.202 Angle : 0.559 6.693 9442 Z= 0.294 Chirality : 0.042 0.134 1112 Planarity : 0.004 0.042 1184 Dihedral : 5.593 80.199 952 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % 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: 1.07 (0.28), residues: 868 helix: 2.09 (0.26), residues: 376 sheet: 0.02 (0.37), residues: 178 loop : -0.54 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.010 0.002 HIS A 220 PHE 0.013 0.002 PHE B 241 TYR 0.012 0.001 TYR A 391 ARG 0.007 0.001 ARG B 304 *********************** 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 : 0.763 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.5912 (mt) REVERT: A 211 LYS cc_start: 0.7080 (mtpt) cc_final: 0.6595 (mmtt) REVERT: A 213 GLN cc_start: 0.4821 (OUTLIER) cc_final: 0.4413 (tp40) REVERT: A 271 ASN cc_start: 0.4855 (m-40) cc_final: 0.4238 (m-40) REVERT: A 274 LYS cc_start: 0.5824 (tttt) cc_final: 0.5494 (ttmp) REVERT: A 280 ARG cc_start: 0.6567 (ttp-110) cc_final: 0.6149 (ttp80) REVERT: A 314 GLU cc_start: 0.5786 (mt-10) cc_final: 0.5251 (mp0) REVERT: A 343 LYS cc_start: 0.7025 (tmtt) cc_final: 0.6694 (ttpt) REVERT: A 371 ASN cc_start: 0.6931 (m-40) cc_final: 0.6567 (m-40) REVERT: A 386 MET cc_start: 0.6166 (ttp) cc_final: 0.5598 (ptm) REVERT: B 19 ARG cc_start: 0.8078 (mmm160) cc_final: 0.7859 (mmm160) REVERT: B 59 TYR cc_start: 0.6618 (m-80) cc_final: 0.6156 (m-80) REVERT: B 226 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.5873 (mp0) REVERT: B 251 ARG cc_start: 0.6076 (mpt180) cc_final: 0.5766 (mmt-90) REVERT: B 314 ARG cc_start: 0.5797 (ttp-170) cc_final: 0.5464 (ttp-170) REVERT: G 19 LEU cc_start: 0.6484 (OUTLIER) cc_final: 0.6111 (mm) REVERT: R 45 ILE cc_start: 0.5574 (pt) cc_final: 0.5349 (mt) REVERT: R 52 PHE cc_start: 0.4641 (t80) cc_final: 0.4080 (t80) REVERT: R 118 THR cc_start: 0.5863 (OUTLIER) cc_final: 0.5644 (m) REVERT: R 235 GLU cc_start: 0.5894 (mm-30) cc_final: 0.5240 (mt-10) REVERT: R 338 TYR cc_start: 0.7092 (m-80) cc_final: 0.6797 (m-10) REVERT: R 346 ARG cc_start: 0.5830 (OUTLIER) cc_final: 0.5132 (tmt170) REVERT: R 374 ASN cc_start: 0.4423 (OUTLIER) cc_final: 0.3910 (m-40) outliers start: 29 outliers final: 12 residues processed: 121 average time/residue: 1.2720 time to fit residues: 161.5876 Evaluate side-chains 118 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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 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 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 118 THR Chi-restraints excluded: chain R residue 172 ILE Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 346 ARG Chi-restraints excluded: chain R residue 362 SER Chi-restraints excluded: chain R residue 374 ASN 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: 8.9990 chunk 52 optimal weight: 0.6980 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.6139 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6946 Z= 0.154 Angle : 0.528 6.732 9442 Z= 0.278 Chirality : 0.041 0.130 1112 Planarity : 0.004 0.039 1184 Dihedral : 5.392 78.522 952 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % 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: 1.25 (0.29), residues: 868 helix: 2.30 (0.27), residues: 376 sheet: 0.05 (0.37), residues: 178 loop : -0.49 (0.35), residues: 314 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 0.018 0.001 PHE R 93 TYR 0.009 0.001 TYR A 391 ARG 0.007 0.000 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 131 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 108 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.5824 (mt) REVERT: A 271 ASN cc_start: 0.4909 (m-40) cc_final: 0.4274 (m-40) REVERT: A 274 LYS cc_start: 0.5811 (tttt) cc_final: 0.5490 (ttmp) REVERT: A 280 ARG cc_start: 0.6508 (ttp-110) cc_final: 0.6066 (ttp80) REVERT: A 314 GLU cc_start: 0.5775 (mt-10) cc_final: 0.5260 (mp0) REVERT: A 343 LYS cc_start: 0.6996 (tmtt) cc_final: 0.6670 (ttpt) REVERT: A 371 ASN cc_start: 0.6910 (m-40) cc_final: 0.6545 (m-40) REVERT: A 386 MET cc_start: 0.6188 (ttp) cc_final: 0.5601 (ptm) REVERT: B 19 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7854 (mmm160) REVERT: B 59 TYR cc_start: 0.6587 (m-80) cc_final: 0.6165 (m-80) REVERT: B 215 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.5753 (mt-10) REVERT: B 219 ARG cc_start: 0.7386 (ttm170) cc_final: 0.6946 (mmt90) REVERT: B 226 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.5954 (mp0) REVERT: B 251 ARG cc_start: 0.6036 (mpt180) cc_final: 0.5764 (mmt-90) REVERT: B 277 SER cc_start: 0.7772 (t) cc_final: 0.7372 (m) REVERT: B 314 ARG cc_start: 0.5775 (ttp-170) cc_final: 0.5434 (ttp-170) REVERT: R 45 ILE cc_start: 0.5518 (pt) cc_final: 0.5299 (mt) REVERT: R 52 PHE cc_start: 0.4651 (t80) cc_final: 0.4067 (t80) REVERT: R 235 GLU cc_start: 0.5824 (mm-30) cc_final: 0.5193 (mt-10) REVERT: R 314 MET cc_start: 0.4432 (tpp) cc_final: 0.4226 (tpp) REVERT: R 338 TYR cc_start: 0.7176 (m-80) cc_final: 0.6940 (m-10) REVERT: R 346 ARG cc_start: 0.5844 (OUTLIER) cc_final: 0.5195 (tmt170) REVERT: R 376 ARG cc_start: 0.6993 (ttm170) cc_final: 0.6675 (mtm-85) outliers start: 23 outliers final: 12 residues processed: 121 average time/residue: 1.2912 time to fit residues: 163.8242 Evaluate side-chains 116 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 MET Chi-restraints excluded: chain A residue 43 LEU 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 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 234 PHE Chi-restraints excluded: chain B residue 267 ASP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 346 ARG 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: 0.8980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 60 optimal weight: 9.9990 chunk 23 optimal weight: 0.0030 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 8.9990 chunk 81 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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 181 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 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 : 0.002 0.026 6946 Z= 0.131 Angle : 0.491 6.916 9442 Z= 0.259 Chirality : 0.040 0.128 1112 Planarity : 0.003 0.038 1184 Dihedral : 5.098 74.764 952 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.54 % Allowed : 20.00 % 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: 1.50 (0.29), residues: 868 helix: 2.53 (0.26), residues: 376 sheet: 0.12 (0.37), residues: 178 loop : -0.35 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.003 0.001 HIS A 362 PHE 0.022 0.001 PHE R 107 TYR 0.007 0.001 TYR G 40 ARG 0.006 0.000 ARG B 304 *********************** 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 128 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.795 Fit side-chains revert: symmetry clash REVERT: A 43 LEU cc_start: 0.6399 (OUTLIER) cc_final: 0.5995 (mt) REVERT: A 271 ASN cc_start: 0.4816 (m-40) cc_final: 0.4173 (m-40) REVERT: A 274 LYS cc_start: 0.5781 (tttt) cc_final: 0.5444 (ttmp) REVERT: A 314 GLU cc_start: 0.5769 (mt-10) cc_final: 0.5247 (mp0) REVERT: A 343 LYS cc_start: 0.7095 (tmtt) cc_final: 0.6766 (ttpt) REVERT: A 371 ASN cc_start: 0.6860 (m-40) cc_final: 0.6485 (m-40) REVERT: A 386 MET cc_start: 0.6085 (ttp) cc_final: 0.5439 (ptp) REVERT: B 19 ARG cc_start: 0.8083 (mmm160) cc_final: 0.7709 (mtp-110) REVERT: B 251 ARG cc_start: 0.6059 (mpt180) cc_final: 0.5775 (mmt-90) REVERT: B 277 SER cc_start: 0.7768 (t) cc_final: 0.7377 (m) REVERT: B 314 ARG cc_start: 0.5716 (ttp-170) cc_final: 0.5357 (ttp-170) REVERT: R 45 ILE cc_start: 0.5493 (pt) cc_final: 0.5275 (mt) REVERT: R 52 PHE cc_start: 0.4587 (t80) cc_final: 0.3995 (t80) REVERT: R 179 TYR cc_start: 0.5915 (m-10) cc_final: 0.5660 (m-10) REVERT: R 235 GLU cc_start: 0.5744 (mm-30) cc_final: 0.5186 (mt-10) REVERT: R 338 TYR cc_start: 0.7101 (m-80) cc_final: 0.6839 (m-10) REVERT: R 346 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.5290 (tpm170) REVERT: R 376 ARG cc_start: 0.7006 (ttm170) cc_final: 0.6741 (mtm-85) outliers start: 18 outliers final: 8 residues processed: 119 average time/residue: 1.2828 time to fit residues: 161.2867 Evaluate side-chains 111 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 101 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 394 VAL Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 223 THR Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 194 ASN Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 215 LEU Chi-restraints excluded: chain R residue 346 ARG 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: 6.9990 chunk 85 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 68 optimal weight: 0.5980 chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- 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 R 181 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 6946 Z= 0.375 Angle : 0.710 10.106 9442 Z= 0.368 Chirality : 0.048 0.146 1112 Planarity : 0.005 0.038 1184 Dihedral : 6.037 80.261 952 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % 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: 0.62 (0.28), residues: 868 helix: 1.55 (0.26), residues: 375 sheet: 0.18 (0.40), residues: 168 loop : -0.76 (0.33), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP B 211 HIS 0.007 0.002 HIS A 357 PHE 0.016 0.002 PHE B 241 TYR 0.019 0.003 TYR R 176 ARG 0.007 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 114 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 95 time to evaluate : 0.750 Fit side-chains revert: symmetry clash REVERT: A 213 GLN cc_start: 0.4962 (OUTLIER) cc_final: 0.4630 (tp40) REVERT: A 314 GLU cc_start: 0.5840 (mt-10) cc_final: 0.5292 (mp0) REVERT: A 343 LYS cc_start: 0.7041 (tmtt) cc_final: 0.6720 (ttpt) REVERT: A 386 MET cc_start: 0.6117 (ttp) cc_final: 0.5665 (ptm) REVERT: B 215 GLU cc_start: 0.5886 (OUTLIER) cc_final: 0.5652 (mt-10) REVERT: B 219 ARG cc_start: 0.7353 (ttm170) cc_final: 0.6954 (mmt90) REVERT: B 314 ARG cc_start: 0.5993 (ttp-170) cc_final: 0.5614 (ttp-170) REVERT: G 19 LEU cc_start: 0.6615 (OUTLIER) cc_final: 0.6226 (mm) REVERT: R 45 ILE cc_start: 0.5540 (pt) cc_final: 0.5317 (mt) REVERT: R 52 PHE cc_start: 0.4869 (t80) cc_final: 0.4389 (t80) REVERT: R 160 LYS cc_start: 0.4505 (mmtp) cc_final: 0.4282 (tmtt) REVERT: R 223 VAL cc_start: 0.5299 (t) cc_final: 0.5035 (t) REVERT: R 235 GLU cc_start: 0.5852 (mm-30) cc_final: 0.5320 (mt-10) REVERT: R 338 TYR cc_start: 0.7225 (m-80) cc_final: 0.6923 (m-10) REVERT: R 346 ARG cc_start: 0.5852 (OUTLIER) cc_final: 0.5194 (tmt170) REVERT: R 376 ARG cc_start: 0.7006 (ttm170) cc_final: 0.6752 (mtm-85) outliers start: 19 outliers final: 10 residues processed: 110 average time/residue: 1.3216 time to fit residues: 152.5015 Evaluate side-chains 106 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.678 ------------------------------------------------------------------------------- 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 223 ASP 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 234 PHE Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain G residue 19 LEU Chi-restraints excluded: chain R residue 208 SER Chi-restraints excluded: chain R residue 320 VAL Chi-restraints excluded: chain R residue 346 ARG 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: 4.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 68 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.200406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.156365 restraints weight = 7073.023| |-----------------------------------------------------------------------------| r_work (start): 0.4006 rms_B_bonded: 2.07 r_work: 0.3883 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.5633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 6946 Z= 0.158 Angle : 0.538 8.312 9442 Z= 0.281 Chirality : 0.041 0.133 1112 Planarity : 0.004 0.043 1184 Dihedral : 5.377 75.280 952 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.83 % Allowed : 22.39 % Favored : 75.77 % 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 (0.29), residues: 868 helix: 2.26 (0.27), residues: 375 sheet: 0.06 (0.38), residues: 179 loop : -0.54 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE B 241 TYR 0.010 0.001 TYR R 179 ARG 0.012 0.001 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3513.12 seconds wall clock time: 61 minutes 47.39 seconds (3707.39 seconds total)