Starting phenix.real_space_refine on Mon Mar 11 18:44:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fls_29285/03_2024/8fls_29285_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fls_29285/03_2024/8fls_29285.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fls_29285/03_2024/8fls_29285.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fls_29285/03_2024/8fls_29285.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fls_29285/03_2024/8fls_29285_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fls_29285/03_2024/8fls_29285_updated.pdb" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.077 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 54 5.16 5 C 5637 2.51 5 N 1543 2.21 5 O 1610 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "R GLU 391": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8844 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1900 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 226} Chain breaks: 2 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 2542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2542 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 5, 'TRANS': 331} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 32 Chain: "G" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 383 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "N" Number of atoms: 953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 953 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 266 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AIB:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2800 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 11, 'TRANS': 350} Chain breaks: 3 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 227 Unresolved non-hydrogen dihedrals: 155 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 115 Time building chain proxies: 4.97, per 1000 atoms: 0.56 Number of scatterers: 8844 At special positions: 0 Unit cell: (73.1, 96.9, 170.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1610 8.00 N 1543 7.00 C 5637 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.01 Simple disulfide: pdb=" SG CYS R 48 " - pdb=" SG CYS R 117 " distance=2.03 Simple disulfide: pdb=" SG CYS R 108 " - pdb=" SG CYS R 148 " distance=2.03 Simple disulfide: pdb=" SG CYS R 131 " - pdb=" SG CYS R 170 " distance=2.03 Simple disulfide: pdb=" SG CYS R 281 " - pdb=" SG CYS R 351 " distance=2.03 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2146 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 11 sheets defined 39.2% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.720A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 51 No H-bonds generated for 'chain 'A' and resid 49 through 51' Processing helix chain 'A' and resid 53 through 62 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 250 through 252 No H-bonds generated for 'chain 'A' and resid 250 through 252' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 302 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 350 removed outlier: 3.867A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 5 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 5.747A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 5.554A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'P' and resid 3 through 31 Processing helix chain 'R' and resid 34 through 53 Processing helix chain 'R' and resid 169 through 171 No H-bonds generated for 'chain 'R' and resid 169 through 171' Processing helix chain 'R' and resid 178 through 211 Processing helix chain 'R' and resid 218 through 243 Processing helix chain 'R' and resid 279 through 311 removed outlier: 4.009A pdb=" N ALA R 284 " --> pdb=" O GLY R 280 " (cutoff:3.500A) Processing helix chain 'R' and resid 317 through 319 No H-bonds generated for 'chain 'R' and resid 317 through 319' Processing helix chain 'R' and resid 321 through 346 Proline residue: R 332 - end of helix Processing helix chain 'R' and resid 358 through 390 removed outlier: 3.644A pdb=" N GLN R 364 " --> pdb=" O TRP R 361 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VAL R 365 " --> pdb=" O ILE R 362 " (cutoff:3.500A) Proline residue: R 366 - end of helix removed outlier: 3.997A pdb=" N VAL R 372 " --> pdb=" O ALA R 369 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN R 374 " --> pdb=" O ILE R 371 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU R 377 " --> pdb=" O ASN R 374 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASN R 380 " --> pdb=" O LEU R 377 " (cutoff:3.500A) Processing helix chain 'R' and resid 400 through 417 Proline residue: R 415 - end of helix Processing helix chain 'R' and resid 419 through 424 Processing helix chain 'R' and resid 435 through 459 removed outlier: 4.548A pdb=" N GLY R 452 " --> pdb=" O ASN R 448 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N PHE R 453 " --> pdb=" O SER R 449 " (cutoff:3.500A) Processing helix chain 'R' and resid 464 through 477 Processing sheet with id= A, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.463A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 60 through 63 removed outlier: 3.864A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.910A 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: 6.788A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.608A 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: 6.774A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.977A 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: 6.977A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.157A 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: 6.760A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.549A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.669A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.075A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 125 through 130 removed outlier: 3.560A pdb=" N GLU R 125 " --> pdb=" O CYS R 148 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N CYS R 148 " --> pdb=" O GLU R 125 " (cutoff:3.500A) 435 hydrogen bonds defined for protein. 1194 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: 2.53 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1484 1.32 - 1.44: 2523 1.44 - 1.57: 4960 1.57 - 1.69: 0 1.69 - 1.81: 74 Bond restraints: 9041 Sorted by residual: bond pdb=" CA SER B 331 " pdb=" CB SER B 331 " ideal model delta sigma weight residual 1.532 1.479 0.053 1.68e-02 3.54e+03 9.89e+00 bond pdb=" C PRO N 100 " pdb=" O PRO N 100 " ideal model delta sigma weight residual 1.237 1.199 0.038 1.26e-02 6.30e+03 9.31e+00 bond pdb=" N THR N 111 " pdb=" CA THR N 111 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.10e-02 8.26e+03 9.27e+00 bond pdb=" N VAL B 71 " pdb=" CA VAL B 71 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.22e+00 bond pdb=" N VAL B 315 " pdb=" CA VAL B 315 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.10e-02 8.26e+03 8.75e+00 ... (remaining 9036 not shown) Histogram of bond angle deviations from ideal: 99.41 - 106.42: 202 106.42 - 113.42: 4885 113.42 - 120.43: 3494 120.43 - 127.43: 3596 127.43 - 134.44: 102 Bond angle restraints: 12279 Sorted by residual: angle pdb=" N HIS R 223 " pdb=" CA HIS R 223 " pdb=" C HIS R 223 " ideal model delta sigma weight residual 110.97 105.65 5.32 1.09e+00 8.42e-01 2.38e+01 angle pdb=" N VAL R 365 " pdb=" CA VAL R 365 " pdb=" CB VAL R 365 " ideal model delta sigma weight residual 110.50 113.45 -2.95 6.30e-01 2.52e+00 2.19e+01 angle pdb=" C PHE R 335 " pdb=" CA PHE R 335 " pdb=" CB PHE R 335 " ideal model delta sigma weight residual 110.85 118.51 -7.66 1.70e+00 3.46e-01 2.03e+01 angle pdb=" N ASP B 76 " pdb=" CA ASP B 76 " pdb=" C ASP B 76 " ideal model delta sigma weight residual 113.15 108.12 5.03 1.19e+00 7.06e-01 1.78e+01 angle pdb=" N ASP B 333 " pdb=" CA ASP B 333 " pdb=" C ASP B 333 " ideal model delta sigma weight residual 113.15 108.15 5.00 1.19e+00 7.06e-01 1.77e+01 ... (remaining 12274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4805 17.73 - 35.47: 407 35.47 - 53.20: 76 53.20 - 70.94: 17 70.94 - 88.67: 7 Dihedral angle restraints: 5312 sinusoidal: 1989 harmonic: 3323 Sorted by residual: dihedral pdb=" C PHE R 335 " pdb=" N PHE R 335 " pdb=" CA PHE R 335 " pdb=" CB PHE R 335 " ideal model delta harmonic sigma weight residual -122.60 -136.96 14.36 0 2.50e+00 1.60e-01 3.30e+01 dihedral pdb=" CB CYS R 281 " pdb=" SG CYS R 281 " pdb=" SG CYS R 351 " pdb=" CB CYS R 351 " ideal model delta sinusoidal sigma weight residual 93.00 138.66 -45.66 1 1.00e+01 1.00e-02 2.89e+01 dihedral pdb=" CA LEU A 291 " pdb=" C LEU A 291 " pdb=" N ASN A 292 " pdb=" CA ASN A 292 " ideal model delta harmonic sigma weight residual -180.00 -155.43 -24.57 0 5.00e+00 4.00e-02 2.42e+01 ... (remaining 5309 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1279 0.095 - 0.190: 86 0.190 - 0.285: 12 0.285 - 0.379: 1 0.379 - 0.474: 1 Chirality restraints: 1379 Sorted by residual: chirality pdb=" CA PHE R 335 " pdb=" N PHE R 335 " pdb=" C PHE R 335 " pdb=" CB PHE R 335 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CA LYS B 57 " pdb=" N LYS B 57 " pdb=" C LYS B 57 " pdb=" CB LYS B 57 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CA ILE B 58 " pdb=" N ILE B 58 " pdb=" C ILE B 58 " pdb=" CB ILE B 58 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 1376 not shown) Planarity restraints: 1563 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR R 427 " 0.060 5.00e-02 4.00e+02 9.13e-02 1.33e+01 pdb=" N PRO R 428 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO R 428 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO R 428 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS R 360 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.08e+00 pdb=" C LYS R 360 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS R 360 " 0.016 2.00e-02 2.50e+03 pdb=" N TRP R 361 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.040 5.00e-02 4.00e+02 6.16e-02 6.07e+00 pdb=" N PRO G 49 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.034 5.00e-02 4.00e+02 ... (remaining 1560 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1670 2.77 - 3.30: 8585 3.30 - 3.84: 15344 3.84 - 4.37: 18229 4.37 - 4.90: 31493 Nonbonded interactions: 75321 Sorted by model distance: nonbonded pdb=" OE2 GLU P 4 " pdb=" OH TYR R 195 " model vdw 2.239 2.440 nonbonded pdb=" OD1 ASP P 17 " pdb=" NH2 ARG P 20 " model vdw 2.255 2.520 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.265 2.440 nonbonded pdb=" O ALA A 48 " pdb=" OG SER A 51 " model vdw 2.304 2.440 nonbonded pdb=" NH2 ARG B 8 " pdb=" OE1 GLN N 120 " model vdw 2.309 2.520 ... (remaining 75316 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=0.00 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: 1.570 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: 5.510 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.970 Find NCS groups from input model: 0.230 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9041 Z= 0.283 Angle : 0.700 7.657 12279 Z= 0.454 Chirality : 0.054 0.474 1379 Planarity : 0.005 0.091 1563 Dihedral : 14.012 88.671 3148 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.11 % Allowed : 1.00 % Favored : 97.89 % Cbeta Deviations : 0.09 % 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: 1.08 (0.25), residues: 1119 helix: 2.25 (0.24), residues: 432 sheet: -0.60 (0.34), residues: 209 loop : -0.02 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 339 HIS 0.007 0.001 HIS A 357 PHE 0.023 0.002 PHE R 447 TYR 0.011 0.001 TYR R 296 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 129 time to evaluate : 0.976 Fit side-chains REVERT: B 59 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.7052 (t80) REVERT: N 105 ARG cc_start: 0.7528 (ttt90) cc_final: 0.7215 (tmt170) outliers start: 10 outliers final: 4 residues processed: 136 average time/residue: 0.2543 time to fit residues: 45.9189 Evaluate side-chains 120 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 115 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain R residue 363 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.5980 chunk 84 optimal weight: 30.0000 chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.9990 chunk 101 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 31 ASN ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.0542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9041 Z= 0.191 Angle : 0.498 6.291 12279 Z= 0.266 Chirality : 0.041 0.202 1379 Planarity : 0.004 0.067 1563 Dihedral : 4.662 54.928 1252 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.11 % Allowed : 7.88 % Favored : 91.01 % 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: 1.16 (0.25), residues: 1119 helix: 2.39 (0.25), residues: 432 sheet: -0.62 (0.34), residues: 213 loop : 0.01 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 339 HIS 0.006 0.001 HIS A 357 PHE 0.035 0.002 PHE R 335 TYR 0.030 0.001 TYR R 191 ARG 0.004 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 121 time to evaluate : 0.956 Fit side-chains REVERT: A 60 MET cc_start: 0.6116 (mtt) cc_final: 0.5914 (mtt) REVERT: A 299 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.6996 (mp0) REVERT: A 378 ASP cc_start: 0.7892 (m-30) cc_final: 0.7643 (m-30) REVERT: B 59 TYR cc_start: 0.7528 (OUTLIER) cc_final: 0.6874 (t80) REVERT: N 34 MET cc_start: 0.8114 (mmm) cc_final: 0.7864 (mmm) REVERT: N 105 ARG cc_start: 0.7415 (ttt90) cc_final: 0.7048 (tmt170) outliers start: 10 outliers final: 6 residues processed: 125 average time/residue: 0.2462 time to fit residues: 41.4680 Evaluate side-chains 118 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 1.9990 chunk 84 optimal weight: 30.0000 chunk 69 optimal weight: 0.0970 chunk 28 optimal weight: 5.9990 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 0.2980 chunk 90 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 81 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6629 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9041 Z= 0.171 Angle : 0.476 6.238 12279 Z= 0.255 Chirality : 0.040 0.162 1379 Planarity : 0.004 0.057 1563 Dihedral : 4.462 51.035 1249 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.11 % Allowed : 9.77 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1119 helix: 2.51 (0.25), residues: 431 sheet: -0.61 (0.34), residues: 211 loop : 0.07 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 339 HIS 0.005 0.001 HIS A 357 PHE 0.031 0.001 PHE R 335 TYR 0.029 0.001 TYR R 191 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.906 Fit side-chains REVERT: A 299 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: A 378 ASP cc_start: 0.7903 (m-30) cc_final: 0.7608 (m-30) REVERT: B 59 TYR cc_start: 0.7584 (OUTLIER) cc_final: 0.7080 (t80) REVERT: N 105 ARG cc_start: 0.7328 (ttt90) cc_final: 0.6958 (tmt170) outliers start: 10 outliers final: 6 residues processed: 121 average time/residue: 0.2358 time to fit residues: 38.6245 Evaluate side-chains 116 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 102 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 29 optimal weight: 0.0970 chunk 90 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 HIS ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6610 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9041 Z= 0.149 Angle : 0.462 6.206 12279 Z= 0.248 Chirality : 0.040 0.223 1379 Planarity : 0.004 0.052 1563 Dihedral : 4.227 50.386 1246 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.11 % Allowed : 11.21 % Favored : 87.68 % 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: 1.40 (0.26), residues: 1119 helix: 2.62 (0.25), residues: 430 sheet: -0.52 (0.33), residues: 213 loop : 0.12 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS A 220 PHE 0.028 0.001 PHE R 335 TYR 0.028 0.001 TYR R 191 ARG 0.005 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 0.949 Fit side-chains REVERT: A 299 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 378 ASP cc_start: 0.7888 (m-30) cc_final: 0.7614 (m-30) REVERT: B 59 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.7195 (t80) REVERT: N 105 ARG cc_start: 0.7325 (ttt90) cc_final: 0.6944 (tmt170) REVERT: R 335 PHE cc_start: 0.6332 (p90) cc_final: 0.5664 (m-80) outliers start: 10 outliers final: 8 residues processed: 120 average time/residue: 0.2601 time to fit residues: 41.3307 Evaluate side-chains 119 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain R residue 302 GLU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 30.0000 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 97 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9041 Z= 0.191 Angle : 0.483 6.262 12279 Z= 0.258 Chirality : 0.041 0.236 1379 Planarity : 0.004 0.053 1563 Dihedral : 4.312 49.537 1246 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.44 % Allowed : 12.65 % Favored : 85.90 % 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 (0.25), residues: 1119 helix: 2.52 (0.25), residues: 431 sheet: -0.59 (0.33), residues: 220 loop : 0.06 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 211 HIS 0.005 0.001 HIS A 220 PHE 0.033 0.001 PHE R 335 TYR 0.027 0.001 TYR R 191 ARG 0.006 0.000 ARG R 476 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 112 time to evaluate : 1.024 Fit side-chains REVERT: A 299 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: A 378 ASP cc_start: 0.7859 (m-30) cc_final: 0.7582 (m-30) REVERT: B 59 TYR cc_start: 0.7558 (OUTLIER) cc_final: 0.7134 (t80) REVERT: N 105 ARG cc_start: 0.7345 (ttt90) cc_final: 0.6933 (tmt170) REVERT: R 335 PHE cc_start: 0.6392 (p90) cc_final: 0.5625 (m-80) outliers start: 13 outliers final: 8 residues processed: 121 average time/residue: 0.2561 time to fit residues: 41.4663 Evaluate side-chains 118 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 0.0010 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9041 Z= 0.200 Angle : 0.493 6.318 12279 Z= 0.264 Chirality : 0.041 0.247 1379 Planarity : 0.004 0.054 1563 Dihedral : 4.365 49.374 1246 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.66 % Allowed : 12.99 % Favored : 85.35 % 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 (0.25), residues: 1119 helix: 2.51 (0.25), residues: 430 sheet: -0.57 (0.33), residues: 220 loop : 0.02 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.005 0.001 HIS A 220 PHE 0.033 0.001 PHE R 335 TYR 0.027 0.001 TYR R 191 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.093 Fit side-chains REVERT: A 299 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: A 378 ASP cc_start: 0.7851 (m-30) cc_final: 0.7563 (m-30) REVERT: B 59 TYR cc_start: 0.7566 (OUTLIER) cc_final: 0.7184 (t80) REVERT: N 105 ARG cc_start: 0.7358 (ttt90) cc_final: 0.6924 (tmt170) REVERT: R 335 PHE cc_start: 0.6433 (p90) cc_final: 0.5635 (m-80) outliers start: 15 outliers final: 11 residues processed: 115 average time/residue: 0.2530 time to fit residues: 38.9056 Evaluate side-chains 120 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 107 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 9.9990 chunk 79 optimal weight: 0.0050 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 0.0040 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.0570 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.3726 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9041 Z= 0.123 Angle : 0.442 6.134 12279 Z= 0.239 Chirality : 0.039 0.249 1379 Planarity : 0.004 0.048 1563 Dihedral : 4.084 48.024 1246 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.66 % Allowed : 12.99 % Favored : 85.35 % 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: 1.49 (0.26), residues: 1119 helix: 2.70 (0.25), residues: 430 sheet: -0.40 (0.32), residues: 223 loop : 0.15 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 PHE 0.033 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.006 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 0.924 Fit side-chains revert: symmetry clash REVERT: A 299 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: A 378 ASP cc_start: 0.7869 (m-30) cc_final: 0.7564 (m-30) REVERT: B 59 TYR cc_start: 0.7434 (OUTLIER) cc_final: 0.7026 (t80) REVERT: R 335 PHE cc_start: 0.6343 (p90) cc_final: 0.5581 (m-80) outliers start: 15 outliers final: 8 residues processed: 125 average time/residue: 0.2529 time to fit residues: 42.5107 Evaluate side-chains 118 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 108 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain R residue 218 THR Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.1223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9041 Z= 0.172 Angle : 0.470 6.230 12279 Z= 0.252 Chirality : 0.040 0.254 1379 Planarity : 0.004 0.051 1563 Dihedral : 4.185 48.288 1246 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.66 % Allowed : 12.99 % Favored : 85.35 % 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: 1.38 (0.26), residues: 1119 helix: 2.64 (0.25), residues: 430 sheet: -0.51 (0.32), residues: 225 loop : 0.09 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 PHE 0.034 0.001 PHE R 335 TYR 0.026 0.001 TYR R 191 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 107 time to evaluate : 1.022 Fit side-chains REVERT: A 299 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7080 (mp0) REVERT: B 59 TYR cc_start: 0.7451 (OUTLIER) cc_final: 0.7031 (t80) REVERT: N 105 ARG cc_start: 0.7277 (ttt90) cc_final: 0.6892 (tmt170) REVERT: R 335 PHE cc_start: 0.6452 (p90) cc_final: 0.5653 (m-80) outliers start: 15 outliers final: 10 residues processed: 118 average time/residue: 0.2603 time to fit residues: 41.2765 Evaluate side-chains 119 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 107 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 40.0000 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6611 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9041 Z= 0.155 Angle : 0.458 6.191 12279 Z= 0.246 Chirality : 0.040 0.254 1379 Planarity : 0.004 0.051 1563 Dihedral : 4.140 47.924 1246 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.55 % Allowed : 13.21 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.26), residues: 1119 helix: 2.63 (0.25), residues: 433 sheet: -0.48 (0.33), residues: 220 loop : 0.11 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 PHE 0.033 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.007 0.000 ARG B 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.992 Fit side-chains REVERT: A 299 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: A 378 ASP cc_start: 0.7832 (m-30) cc_final: 0.7531 (m-30) REVERT: B 59 TYR cc_start: 0.7456 (OUTLIER) cc_final: 0.7015 (t80) REVERT: N 105 ARG cc_start: 0.7261 (ttt90) cc_final: 0.6866 (tmt170) REVERT: R 335 PHE cc_start: 0.6426 (p90) cc_final: 0.5639 (m-80) REVERT: R 447 PHE cc_start: 0.4630 (OUTLIER) cc_final: 0.4061 (m-10) outliers start: 14 outliers final: 10 residues processed: 120 average time/residue: 0.2511 time to fit residues: 40.4072 Evaluate side-chains 119 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 447 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6626 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9041 Z= 0.171 Angle : 0.470 6.220 12279 Z= 0.251 Chirality : 0.040 0.264 1379 Planarity : 0.004 0.051 1563 Dihedral : 4.182 47.989 1246 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.66 % Allowed : 13.32 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1119 helix: 2.63 (0.25), residues: 430 sheet: -0.53 (0.33), residues: 222 loop : 0.11 (0.30), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.006 0.001 HIS A 220 PHE 0.034 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.007 0.000 ARG B 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2238 Ramachandran restraints generated. 1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.156 Fit side-chains REVERT: A 299 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: B 59 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.7022 (t80) REVERT: N 105 ARG cc_start: 0.7268 (ttt90) cc_final: 0.6861 (tmt170) REVERT: R 335 PHE cc_start: 0.6490 (p90) cc_final: 0.5656 (m-80) REVERT: R 447 PHE cc_start: 0.4659 (OUTLIER) cc_final: 0.4101 (m-10) outliers start: 15 outliers final: 12 residues processed: 120 average time/residue: 0.2495 time to fit residues: 40.2212 Evaluate side-chains 124 residues out of total 983 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 125 ASN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain N residue 45 LEU Chi-restraints excluded: chain N residue 109 ASP Chi-restraints excluded: chain R residue 363 ILE Chi-restraints excluded: chain R residue 430 THR Chi-restraints excluded: chain R residue 447 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 11 optimal weight: 0.0070 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 50.0000 chunk 5 optimal weight: 1.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.193732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154618 restraints weight = 9557.606| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 1.93 r_work: 0.3608 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9041 Z= 0.136 Angle : 0.447 6.158 12279 Z= 0.240 Chirality : 0.040 0.250 1379 Planarity : 0.004 0.049 1563 Dihedral : 4.053 47.312 1246 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.66 % Allowed : 13.32 % Favored : 85.02 % 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: 1.53 (0.26), residues: 1119 helix: 2.70 (0.25), residues: 432 sheet: -0.40 (0.33), residues: 218 loop : 0.20 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 298 HIS 0.005 0.001 HIS A 220 PHE 0.033 0.001 PHE R 335 TYR 0.025 0.001 TYR R 191 ARG 0.007 0.000 ARG B 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2177.87 seconds wall clock time: 40 minutes 3.29 seconds (2403.29 seconds total)