Starting phenix.real_space_refine on Sun Apr 7 22:23:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrv_36607/04_2024/8jrv_36607_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrv_36607/04_2024/8jrv_36607.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrv_36607/04_2024/8jrv_36607_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrv_36607/04_2024/8jrv_36607_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrv_36607/04_2024/8jrv_36607_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrv_36607/04_2024/8jrv_36607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrv_36607/04_2024/8jrv_36607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrv_36607/04_2024/8jrv_36607_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jrv_36607/04_2024/8jrv_36607_updated.pdb" } resolution = 3.3 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= 0.006 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4023 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 21 5.16 5 C 4933 2.51 5 N 1307 2.21 5 O 1438 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 6": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 7707 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 2338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2338 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'PTRANS': 5, 'TRANS': 313} Chain breaks: 4 Unresolved non-hydrogen bonds: 276 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 251 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 5, 'TPO:plan-1': 1, 'ARG:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 3, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 6, 'HIS:plan': 3} Unresolved non-hydrogen planarities: 164 Chain: "G" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 168 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 49 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 2632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 355, 2632 Classifications: {'peptide': 355} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 28, 'TRANS': 326} Chain breaks: 1 Unresolved non-hydrogen bonds: 193 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 159 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 14, 'ARG:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 111 Chain: "H" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 114} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 788 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 855 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 110} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 4.35, per 1000 atoms: 0.56 Number of scatterers: 7707 At special positions: 0 Unit cell: (96.39, 97.461, 164.934, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 8 15.00 O 1438 8.00 N 1307 7.00 C 4933 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 224 " - pdb=" SG CYS R 294 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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: 3.42 Conformation dependent library (CDL) restraints added in 1.5 seconds 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1936 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 19 helices and 14 sheets defined 27.9% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.49 Creating SS restraints... Processing helix chain 'R' and resid 28 through 46 Processing helix chain 'R' and resid 128 through 165 removed outlier: 3.727A pdb=" N SER R 140 " --> pdb=" O LYS R 136 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR R 145 " --> pdb=" O PHE R 141 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N GLY R 148 " --> pdb=" O MET R 144 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 170 removed outlier: 3.946A pdb=" N HIS R 170 " --> pdb=" O SER R 167 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 172 through 206 removed outlier: 4.463A pdb=" N HIS R 177 " --> pdb=" O ARG R 173 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA R 178 " --> pdb=" O ASN R 174 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER R 183 " --> pdb=" O ASN R 179 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE R 184 " --> pdb=" O LEU R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 253 removed outlier: 3.543A pdb=" N TYR R 239 " --> pdb=" O ILE R 235 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU R 242 " --> pdb=" O ASN R 238 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN R 251 " --> pdb=" O LEU R 247 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU R 252 " --> pdb=" O TYR R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 271 removed outlier: 3.562A pdb=" N LEU R 268 " --> pdb=" O PHE R 264 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY R 269 " --> pdb=" O SER R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 274 through 277 No H-bonds generated for 'chain 'R' and resid 274 through 277' Processing helix chain 'R' and resid 280 through 287 removed outlier: 3.666A pdb=" N CYS R 287 " --> pdb=" O ALA R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 304 through 336 removed outlier: 4.032A pdb=" N ARG R 308 " --> pdb=" O TRP R 305 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N PHE R 309 " --> pdb=" O ILE R 306 " (cutoff:3.500A) Proline residue: R 310 - end of helix removed outlier: 3.621A pdb=" N LEU R 313 " --> pdb=" O PRO R 310 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE R 317 " --> pdb=" O ALA R 314 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL R 323 " --> pdb=" O PHE R 320 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE R 325 " --> pdb=" O PHE R 322 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL R 326 " --> pdb=" O VAL R 323 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN R 327 " --> pdb=" O ARG R 324 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU R 329 " --> pdb=" O VAL R 326 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL R 330 " --> pdb=" O GLN R 327 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA R 331 " --> pdb=" O LEU R 328 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG R 334 " --> pdb=" O ALA R 331 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA R 335 " --> pdb=" O LYS R 332 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ARG R 336 " --> pdb=" O LEU R 333 " (cutoff:3.500A) Processing helix chain 'R' and resid 343 through 366 removed outlier: 3.849A pdb=" N ALA R 348 " --> pdb=" O LYS R 344 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR R 353 " --> pdb=" O LYS R 349 " (cutoff:3.500A) Proline residue: R 356 - end of helix removed outlier: 3.551A pdb=" N HIS R 361 " --> pdb=" O LEU R 357 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLU R 362 " --> pdb=" O LEU R 358 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL R 363 " --> pdb=" O GLY R 359 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE R 365 " --> pdb=" O HIS R 361 " (cutoff:3.500A) Processing helix chain 'R' and resid 380 through 390 Processing helix chain 'R' and resid 392 through 401 Processing helix chain 'R' and resid 405 through 424 removed outlier: 3.505A pdb=" N ARG R 414 " --> pdb=" O GLU R 410 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS R 422 " --> pdb=" O TRP R 418 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N VAL R 423 " --> pdb=" O ARG R 419 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 24 removed outlier: 3.582A pdb=" N PHE G 6 " --> pdb=" O SER G 2 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER G 11 " --> pdb=" O THR G 7 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS G 12 " --> pdb=" O SER G 8 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N TYR G 13 " --> pdb=" O ASP G 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 108 removed outlier: 3.617A pdb=" N LYS A 106 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS A 107 " --> pdb=" O ARG A 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'B' and resid 61 through 63 No H-bonds generated for 'chain 'B' and resid 61 through 63' Processing helix chain 'B' and resid 74 through 76 No H-bonds generated for 'chain 'B' and resid 74 through 76' Processing sheet with id= A, first strand: chain 'A' and resid 9 through 12 removed outlier: 3.578A pdb=" N VAL A 20 " --> pdb=" O LYS A 11 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 7.071A pdb=" N GLU A 169 " --> pdb=" O PHE A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.790A pdb=" N ALA A 148 " --> pdb=" O VAL A 164 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 142 through 144 removed outlier: 3.729A pdb=" N ASP A 143 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA A 60 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N PHE A 80 " --> pdb=" O ALA A 59 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N PHE A 61 " --> pdb=" O ASP A 78 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASP A 78 " --> pdb=" O PHE A 61 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 127 through 129 Processing sheet with id= F, first strand: chain 'A' and resid 183 through 188 removed outlier: 3.939A pdb=" N ALA A 201 " --> pdb=" O ALA A 184 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A 186 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LEU A 199 " --> pdb=" O THR A 186 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU A 197 " --> pdb=" O ARG A 188 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N HIS A 198 " --> pdb=" O THR A 221 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 342 through 349 removed outlier: 3.556A pdb=" N VAL A 325 " --> pdb=" O VAL A 345 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 258 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 8 through 10 Processing sheet with id= I, first strand: chain 'H' and resid 117 through 119 removed outlier: 3.763A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.580A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'L' and resid 86 through 88 removed outlier: 3.612A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 63 through 68 removed outlier: 3.804A pdb=" N ASP L 71 " --> pdb=" O SER L 68 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 4 through 7 removed outlier: 3.734A pdb=" N THR B 77 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP B 72 " --> pdb=" O THR B 77 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 108 through 110 removed outlier: 4.342A pdb=" N THR B 108 " --> pdb=" O TYR B 93 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) 297 hydrogen bonds defined for protein. 798 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: 2.20 Time building geometry restraints manager: 3.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1354 1.33 - 1.45: 2110 1.45 - 1.58: 4364 1.58 - 1.70: 23 1.70 - 1.82: 28 Bond restraints: 7879 Sorted by residual: bond pdb=" OG1 TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.717 1.619 0.098 2.00e-02 2.50e+03 2.39e+01 bond pdb=" O1P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.525 1.612 -0.087 2.00e-02 2.50e+03 1.88e+01 bond pdb=" O3P TPO R1360 " pdb=" P TPO R1360 " ideal model delta sigma weight residual 1.528 1.612 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" O13 PIO A 701 " pdb=" P1 PIO A 701 " ideal model delta sigma weight residual 1.648 1.589 0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C1A PIO A 701 " pdb=" O2C PIO A 701 " ideal model delta sigma weight residual 1.399 1.341 0.058 2.00e-02 2.50e+03 8.47e+00 ... (remaining 7874 not shown) Histogram of bond angle deviations from ideal: 90.81 - 99.96: 3 99.96 - 109.11: 535 109.11 - 118.26: 5565 118.26 - 127.41: 4580 127.41 - 136.56: 87 Bond angle restraints: 10770 Sorted by residual: angle pdb=" O1 PIO A 701 " pdb=" P1 PIO A 701 " pdb=" O13 PIO A 701 " ideal model delta sigma weight residual 109.47 90.81 18.66 3.00e+00 1.11e-01 3.87e+01 angle pdb=" C5 PIO A 701 " pdb=" O5 PIO A 701 " pdb=" P5 PIO A 701 " ideal model delta sigma weight residual 118.46 136.56 -18.10 3.00e+00 1.11e-01 3.64e+01 angle pdb=" C2C PIO A 701 " pdb=" C1C PIO A 701 " pdb=" O13 PIO A 701 " ideal model delta sigma weight residual 109.47 92.93 16.54 3.00e+00 1.11e-01 3.04e+01 angle pdb=" N ILE R 270 " pdb=" CA ILE R 270 " pdb=" C ILE R 270 " ideal model delta sigma weight residual 113.53 109.00 4.53 9.80e-01 1.04e+00 2.13e+01 angle pdb=" C5 PIO A 701 " pdb=" C4 PIO A 701 " pdb=" O4 PIO A 701 " ideal model delta sigma weight residual 108.86 96.34 12.52 3.00e+00 1.11e-01 1.74e+01 ... (remaining 10765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.50: 4348 23.50 - 47.00: 219 47.00 - 70.51: 26 70.51 - 94.01: 9 94.01 - 117.51: 1 Dihedral angle restraints: 4603 sinusoidal: 1594 harmonic: 3009 Sorted by residual: dihedral pdb=" CB CYS L 24 " pdb=" SG CYS L 24 " pdb=" SG CYS L 89 " pdb=" CB CYS L 89 " ideal model delta sinusoidal sigma weight residual 93.00 166.90 -73.90 1 1.00e+01 1.00e-02 6.94e+01 dihedral pdb=" CA VAL R 292 " pdb=" C VAL R 292 " pdb=" N GLN R 293 " pdb=" CA GLN R 293 " ideal model delta harmonic sigma weight residual 180.00 157.72 22.28 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" C1 PIO A 701 " pdb=" C2 PIO A 701 " pdb=" C3 PIO A 701 " pdb=" C4 PIO A 701 " ideal model delta sinusoidal sigma weight residual 52.96 -64.55 117.51 1 3.00e+01 1.11e-03 1.56e+01 ... (remaining 4600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1128 0.063 - 0.126: 125 0.126 - 0.189: 6 0.189 - 0.252: 1 0.252 - 0.315: 1 Chirality restraints: 1261 Sorted by residual: chirality pdb=" C4 PIO A 701 " pdb=" C3 PIO A 701 " pdb=" C5 PIO A 701 " pdb=" O4 PIO A 701 " both_signs ideal model delta sigma weight residual False 2.50 2.82 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C2C PIO A 701 " pdb=" C1C PIO A 701 " pdb=" C3C PIO A 701 " pdb=" O2C PIO A 701 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB THR B 90 " pdb=" CA THR B 90 " pdb=" OG1 THR B 90 " pdb=" CG2 THR B 90 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.23e-01 ... (remaining 1258 not shown) Planarity restraints: 1356 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 258 " -0.030 5.00e-02 4.00e+02 4.48e-02 3.22e+00 pdb=" N PRO R 259 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 259 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 259 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 88 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 89 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA R 274 " -0.022 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO R 275 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO R 275 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO R 275 " -0.018 5.00e-02 4.00e+02 ... (remaining 1353 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1599 2.78 - 3.31: 7292 3.31 - 3.84: 12077 3.84 - 4.37: 13215 4.37 - 4.90: 23208 Nonbonded interactions: 57391 Sorted by model distance: nonbonded pdb=" O MET B 82 " pdb=" ND2 ASN B 83 " model vdw 2.250 2.520 nonbonded pdb=" OD2 ASP A 204 " pdb=" OG SER A 215 " model vdw 2.275 2.440 nonbonded pdb=" NH1 ARG H 70 " pdb=" O SER H 88 " model vdw 2.294 2.520 nonbonded pdb=" O2P SEP R1363 " pdb=" OH TYR A 21 " model vdw 2.295 2.440 nonbonded pdb=" OD2 ASP A 297 " pdb=" OH TYR H 60 " model vdw 2.315 2.440 ... (remaining 57386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 3.820 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.900 Find NCS groups from input model: 0.240 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 7879 Z= 0.233 Angle : 0.711 18.660 10770 Z= 0.313 Chirality : 0.041 0.315 1261 Planarity : 0.004 0.045 1356 Dihedral : 13.978 117.509 2658 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % 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: -0.16 (0.27), residues: 1005 helix: 0.79 (0.30), residues: 272 sheet: 0.43 (0.32), residues: 286 loop : -0.99 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 241 HIS 0.002 0.000 HIS A 219 PHE 0.023 0.001 PHE R 289 TYR 0.007 0.001 TYR B 37 ARG 0.014 0.001 ARG H 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 256 time to evaluate : 0.823 Fit side-chains REVERT: R 141 PHE cc_start: 0.7678 (m-80) cc_final: 0.7256 (m-80) REVERT: R 197 LEU cc_start: 0.8448 (mt) cc_final: 0.8213 (mt) REVERT: R 232 GLN cc_start: 0.8355 (mm-40) cc_final: 0.8087 (mm110) REVERT: A 122 ASN cc_start: 0.8646 (t0) cc_final: 0.8398 (t0) REVERT: A 145 GLU cc_start: 0.7606 (tt0) cc_final: 0.7061 (tt0) REVERT: A 185 GLU cc_start: 0.6350 (tp30) cc_final: 0.6109 (tp30) REVERT: A 222 ASN cc_start: 0.7441 (t160) cc_final: 0.6976 (t0) REVERT: A 225 ASN cc_start: 0.7988 (p0) cc_final: 0.7772 (p0) REVERT: A 255 MET cc_start: 0.7163 (tmm) cc_final: 0.6930 (tmm) REVERT: L 12 LEU cc_start: 0.8417 (mm) cc_final: 0.8087 (mm) REVERT: B 46 GLU cc_start: 0.6164 (pp20) cc_final: 0.5906 (pp20) REVERT: B 65 ASP cc_start: 0.8393 (t0) cc_final: 0.7823 (t0) outliers start: 0 outliers final: 0 residues processed: 256 average time/residue: 0.1830 time to fit residues: 63.3549 Evaluate side-chains 222 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 90 optimal weight: 0.4980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN A 219 HIS ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7879 Z= 0.245 Angle : 0.629 9.217 10770 Z= 0.326 Chirality : 0.041 0.182 1261 Planarity : 0.004 0.038 1356 Dihedral : 6.989 97.020 1147 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.37 % Favored : 94.53 % Rotamer: Outliers : 2.41 % Allowed : 12.57 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.27), residues: 1005 helix: 0.82 (0.30), residues: 277 sheet: 0.25 (0.31), residues: 308 loop : -0.93 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 104 HIS 0.004 0.001 HIS A 219 PHE 0.017 0.002 PHE R 263 TYR 0.013 0.001 TYR B 79 ARG 0.005 0.001 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 228 time to evaluate : 0.898 Fit side-chains revert: symmetry clash REVERT: R 141 PHE cc_start: 0.7434 (m-80) cc_final: 0.7011 (m-80) REVERT: R 179 ASN cc_start: 0.7770 (m-40) cc_final: 0.7566 (t0) REVERT: R 225 ARG cc_start: 0.6119 (ttp-170) cc_final: 0.5700 (mtm110) REVERT: R 250 HIS cc_start: 0.8431 (OUTLIER) cc_final: 0.8207 (t-90) REVERT: R 259 PRO cc_start: 0.7712 (Cg_endo) cc_final: 0.7495 (Cg_exo) REVERT: A 122 ASN cc_start: 0.8713 (t0) cc_final: 0.8427 (t0) REVERT: A 222 ASN cc_start: 0.7726 (t0) cc_final: 0.7082 (t0) REVERT: A 225 ASN cc_start: 0.8038 (p0) cc_final: 0.7807 (p0) REVERT: A 256 GLU cc_start: 0.8054 (tp30) cc_final: 0.7782 (tp30) REVERT: H 60 TYR cc_start: 0.7458 (m-10) cc_final: 0.7214 (m-10) REVERT: L 83 ASP cc_start: 0.7947 (m-30) cc_final: 0.7679 (m-30) REVERT: B 63 VAL cc_start: 0.8233 (t) cc_final: 0.7763 (p) REVERT: B 65 ASP cc_start: 0.8505 (t0) cc_final: 0.8063 (t0) REVERT: B 81 GLN cc_start: 0.7071 (tp40) cc_final: 0.6807 (tp40) outliers start: 18 outliers final: 13 residues processed: 238 average time/residue: 0.1858 time to fit residues: 59.6584 Evaluate side-chains 239 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 225 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 250 HIS Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 25 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 318 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN B 3 GLN ** B 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 7879 Z= 0.367 Angle : 0.672 9.761 10770 Z= 0.349 Chirality : 0.042 0.184 1261 Planarity : 0.004 0.043 1356 Dihedral : 7.145 94.906 1147 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 4.01 % Allowed : 18.05 % Favored : 77.94 % 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: -0.32 (0.27), residues: 1005 helix: 0.78 (0.30), residues: 273 sheet: 0.01 (0.31), residues: 298 loop : -0.94 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 104 HIS 0.006 0.001 HIS A 362 PHE 0.019 0.002 PHE G 6 TYR 0.020 0.002 TYR R 145 ARG 0.011 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 0.924 Fit side-chains REVERT: R 141 PHE cc_start: 0.7569 (m-80) cc_final: 0.7132 (m-80) REVERT: R 186 LEU cc_start: 0.8664 (tp) cc_final: 0.8443 (tt) REVERT: R 259 PRO cc_start: 0.7811 (Cg_endo) cc_final: 0.7560 (Cg_exo) REVERT: R 405 LYS cc_start: 0.8848 (pttt) cc_final: 0.8560 (pttt) REVERT: A 83 ASN cc_start: 0.8544 (m-40) cc_final: 0.8246 (t0) REVERT: A 122 ASN cc_start: 0.8794 (t0) cc_final: 0.8533 (t0) REVERT: A 222 ASN cc_start: 0.7761 (t0) cc_final: 0.7423 (t0) REVERT: A 250 LYS cc_start: 0.8317 (mmmt) cc_final: 0.8107 (mmtm) REVERT: A 256 GLU cc_start: 0.8207 (tp30) cc_final: 0.7935 (tp30) REVERT: A 257 GLU cc_start: 0.7521 (mm-30) cc_final: 0.6903 (mm-30) REVERT: A 367 GLU cc_start: 0.7922 (tp30) cc_final: 0.7691 (tp30) REVERT: L 37 TYR cc_start: 0.8824 (m-80) cc_final: 0.8379 (m-80) REVERT: L 83 ASP cc_start: 0.8088 (m-30) cc_final: 0.7806 (m-30) REVERT: L 91 GLN cc_start: 0.9035 (pp30) cc_final: 0.8343 (pp30) REVERT: B 6 GLU cc_start: 0.7666 (pp20) cc_final: 0.7279 (pp20) REVERT: B 63 VAL cc_start: 0.8401 (t) cc_final: 0.7962 (p) REVERT: B 81 GLN cc_start: 0.7178 (tp40) cc_final: 0.6706 (tp40) REVERT: B 82 MET cc_start: 0.7943 (mmt) cc_final: 0.7664 (mmt) REVERT: B 108 THR cc_start: 0.7630 (OUTLIER) cc_final: 0.7198 (p) outliers start: 30 outliers final: 24 residues processed: 252 average time/residue: 0.1922 time to fit residues: 65.0249 Evaluate side-chains 248 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 223 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 5.9990 chunk 43 optimal weight: 0.0040 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.1194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 298 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN H 85 GLN B 3 GLN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7879 Z= 0.246 Angle : 0.645 9.697 10770 Z= 0.320 Chirality : 0.041 0.167 1261 Planarity : 0.004 0.044 1356 Dihedral : 6.976 92.195 1147 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.37 % Favored : 93.53 % Rotamer: Outliers : 4.55 % Allowed : 21.12 % Favored : 74.33 % 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: -0.31 (0.27), residues: 1005 helix: 1.02 (0.31), residues: 275 sheet: -0.08 (0.31), residues: 299 loop : -1.05 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP R 241 HIS 0.007 0.001 HIS A 362 PHE 0.024 0.001 PHE G 6 TYR 0.013 0.001 TYR H 107 ARG 0.006 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 233 time to evaluate : 0.907 Fit side-chains REVERT: R 141 PHE cc_start: 0.7586 (m-80) cc_final: 0.7349 (m-80) REVERT: R 186 LEU cc_start: 0.8640 (tp) cc_final: 0.8430 (tt) REVERT: R 229 VAL cc_start: 0.8913 (t) cc_final: 0.8631 (p) REVERT: R 259 PRO cc_start: 0.7879 (Cg_endo) cc_final: 0.7612 (Cg_exo) REVERT: A 122 ASN cc_start: 0.8774 (t0) cc_final: 0.8515 (t0) REVERT: A 222 ASN cc_start: 0.7757 (t0) cc_final: 0.6968 (t0) REVERT: A 256 GLU cc_start: 0.8194 (tp30) cc_final: 0.7967 (tp30) REVERT: A 257 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7054 (mm-30) REVERT: A 367 GLU cc_start: 0.8010 (tp30) cc_final: 0.7763 (tp30) REVERT: L 37 TYR cc_start: 0.8816 (m-80) cc_final: 0.8456 (m-80) REVERT: L 83 ASP cc_start: 0.8073 (m-30) cc_final: 0.7790 (m-30) REVERT: B 3 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8383 (pm20) REVERT: B 43 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8991 (mmtm) REVERT: B 63 VAL cc_start: 0.8323 (OUTLIER) cc_final: 0.7878 (p) outliers start: 34 outliers final: 27 residues processed: 251 average time/residue: 0.1941 time to fit residues: 65.3114 Evaluate side-chains 262 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 3 GLN Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 9.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 0.0770 chunk 82 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN B 3 GLN B 83 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7879 Z= 0.250 Angle : 0.650 9.654 10770 Z= 0.321 Chirality : 0.041 0.173 1261 Planarity : 0.004 0.043 1356 Dihedral : 6.938 91.311 1147 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.27 % Favored : 93.63 % Rotamer: Outliers : 5.08 % Allowed : 22.59 % Favored : 72.33 % 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: -0.24 (0.27), residues: 1005 helix: 1.16 (0.31), residues: 272 sheet: -0.09 (0.30), residues: 304 loop : -1.01 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 241 HIS 0.006 0.001 HIS A 362 PHE 0.023 0.002 PHE G 6 TYR 0.015 0.001 TYR G 13 ARG 0.004 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 240 time to evaluate : 0.843 Fit side-chains REVERT: R 141 PHE cc_start: 0.7370 (m-80) cc_final: 0.6829 (m-80) REVERT: R 186 LEU cc_start: 0.8633 (tp) cc_final: 0.8427 (tt) REVERT: R 229 VAL cc_start: 0.8897 (t) cc_final: 0.8615 (p) REVERT: R 259 PRO cc_start: 0.7967 (Cg_endo) cc_final: 0.7754 (Cg_exo) REVERT: R 405 LYS cc_start: 0.8808 (pttt) cc_final: 0.8562 (pttt) REVERT: A 83 ASN cc_start: 0.8446 (m-40) cc_final: 0.8083 (t0) REVERT: A 122 ASN cc_start: 0.8777 (t0) cc_final: 0.8517 (t0) REVERT: A 222 ASN cc_start: 0.7762 (t0) cc_final: 0.6973 (t0) REVERT: A 250 LYS cc_start: 0.8492 (mmtm) cc_final: 0.8281 (tppt) REVERT: A 256 GLU cc_start: 0.8201 (tp30) cc_final: 0.7962 (tp30) REVERT: A 257 GLU cc_start: 0.7441 (mm-30) cc_final: 0.7055 (mm-30) REVERT: L 37 TYR cc_start: 0.8809 (m-80) cc_final: 0.8473 (m-80) REVERT: L 83 ASP cc_start: 0.8073 (m-30) cc_final: 0.7774 (m-30) REVERT: L 91 GLN cc_start: 0.8908 (pp30) cc_final: 0.8317 (pp30) REVERT: B 19 ARG cc_start: 0.7851 (tpp-160) cc_final: 0.7634 (mmm-85) REVERT: B 43 LYS cc_start: 0.9336 (mmtt) cc_final: 0.9022 (mmtm) REVERT: B 63 VAL cc_start: 0.8326 (t) cc_final: 0.7879 (p) REVERT: B 77 THR cc_start: 0.8106 (p) cc_final: 0.7808 (p) REVERT: B 83 ASN cc_start: 0.8187 (m-40) cc_final: 0.7818 (m-40) REVERT: B 95 CYS cc_start: 0.7492 (p) cc_final: 0.7168 (p) outliers start: 38 outliers final: 30 residues processed: 263 average time/residue: 0.1884 time to fit residues: 66.3251 Evaluate side-chains 267 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 237 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 398 VAL Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 10 optimal weight: 0.0670 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN B 3 GLN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7879 Z= 0.321 Angle : 0.679 9.764 10770 Z= 0.338 Chirality : 0.042 0.180 1261 Planarity : 0.004 0.044 1356 Dihedral : 7.039 91.389 1147 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.67 % Favored : 93.23 % Rotamer: Outliers : 5.48 % Allowed : 22.59 % Favored : 71.93 % 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: -0.25 (0.27), residues: 1005 helix: 1.19 (0.31), residues: 267 sheet: -0.11 (0.30), residues: 307 loop : -1.02 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP R 241 HIS 0.007 0.001 HIS A 362 PHE 0.027 0.002 PHE G 6 TYR 0.017 0.001 TYR G 13 ARG 0.005 0.000 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 239 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: R 141 PHE cc_start: 0.7503 (m-80) cc_final: 0.6889 (m-80) REVERT: R 229 VAL cc_start: 0.8925 (t) cc_final: 0.8633 (p) REVERT: R 259 PRO cc_start: 0.8052 (Cg_endo) cc_final: 0.7835 (Cg_exo) REVERT: A 122 ASN cc_start: 0.8806 (t0) cc_final: 0.8535 (t0) REVERT: A 185 GLU cc_start: 0.6464 (tp30) cc_final: 0.6224 (tp30) REVERT: A 200 GLU cc_start: 0.6746 (mm-30) cc_final: 0.6544 (mm-30) REVERT: A 222 ASN cc_start: 0.7838 (t0) cc_final: 0.7058 (t0) REVERT: A 250 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8331 (tppt) REVERT: A 256 GLU cc_start: 0.8237 (tp30) cc_final: 0.7989 (tp30) REVERT: A 257 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7051 (mm-30) REVERT: H 9 GLU cc_start: 0.8080 (pm20) cc_final: 0.7525 (pm20) REVERT: L 37 TYR cc_start: 0.8834 (m-80) cc_final: 0.8504 (m-80) REVERT: L 53 SER cc_start: 0.8919 (m) cc_final: 0.8513 (p) REVERT: L 83 ASP cc_start: 0.8129 (m-30) cc_final: 0.7838 (m-30) REVERT: L 91 GLN cc_start: 0.8977 (pp30) cc_final: 0.8408 (pp30) REVERT: B 19 ARG cc_start: 0.7896 (tpp-160) cc_final: 0.7620 (mmm-85) REVERT: B 43 LYS cc_start: 0.9345 (mmtt) cc_final: 0.9079 (mmtm) REVERT: B 63 VAL cc_start: 0.8360 (OUTLIER) cc_final: 0.7907 (p) REVERT: B 77 THR cc_start: 0.8014 (p) cc_final: 0.7770 (p) REVERT: B 83 ASN cc_start: 0.8269 (m-40) cc_final: 0.7922 (m110) outliers start: 41 outliers final: 34 residues processed: 262 average time/residue: 0.1976 time to fit residues: 69.0222 Evaluate side-chains 271 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 236 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 255 LEU Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 54 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 80 ASN B 3 GLN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7879 Z= 0.222 Angle : 0.672 10.087 10770 Z= 0.325 Chirality : 0.041 0.190 1261 Planarity : 0.004 0.044 1356 Dihedral : 6.967 90.496 1147 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.97 % Favored : 93.93 % Rotamer: Outliers : 5.35 % Allowed : 23.53 % Favored : 71.12 % 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: -0.24 (0.27), residues: 1005 helix: 1.24 (0.31), residues: 268 sheet: -0.13 (0.30), residues: 297 loop : -1.02 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 241 HIS 0.006 0.001 HIS A 362 PHE 0.031 0.001 PHE G 6 TYR 0.012 0.001 TYR G 10 ARG 0.003 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 243 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: R 141 PHE cc_start: 0.7581 (m-80) cc_final: 0.6937 (m-80) REVERT: R 173 ARG cc_start: 0.7925 (ttp80) cc_final: 0.7518 (ttp80) REVERT: R 259 PRO cc_start: 0.7997 (Cg_endo) cc_final: 0.7751 (Cg_exo) REVERT: R 304 TRP cc_start: 0.8278 (OUTLIER) cc_final: 0.7795 (m-10) REVERT: R 352 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8387 (mm) REVERT: A 24 LYS cc_start: 0.9078 (pttm) cc_final: 0.8495 (pttm) REVERT: A 122 ASN cc_start: 0.8791 (t0) cc_final: 0.8515 (t0) REVERT: A 200 GLU cc_start: 0.6668 (mm-30) cc_final: 0.6394 (mm-30) REVERT: A 222 ASN cc_start: 0.7824 (t0) cc_final: 0.7052 (t0) REVERT: A 256 GLU cc_start: 0.8167 (tp30) cc_final: 0.7868 (tp30) REVERT: A 257 GLU cc_start: 0.7376 (mm-30) cc_final: 0.6922 (mm-30) REVERT: H 9 GLU cc_start: 0.8039 (pm20) cc_final: 0.7562 (pm20) REVERT: H 60 TYR cc_start: 0.7521 (m-10) cc_final: 0.7170 (m-10) REVERT: H 80 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8372 (t0) REVERT: L 53 SER cc_start: 0.8878 (m) cc_final: 0.8478 (p) REVERT: L 83 ASP cc_start: 0.8146 (m-30) cc_final: 0.7857 (m-30) REVERT: L 91 GLN cc_start: 0.8927 (pp30) cc_final: 0.8352 (pp30) REVERT: B 19 ARG cc_start: 0.7848 (tpp-160) cc_final: 0.7548 (mmm-85) REVERT: B 63 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.7866 (p) REVERT: B 77 THR cc_start: 0.7991 (p) cc_final: 0.7736 (p) outliers start: 40 outliers final: 28 residues processed: 261 average time/residue: 0.1907 time to fit residues: 66.7515 Evaluate side-chains 266 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 234 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 179 ASN Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 316 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 89 optimal weight: 0.0060 overall best weight: 2.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 46 ASN A 222 ASN H 80 ASN B 3 GLN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.4094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7879 Z= 0.418 Angle : 0.749 10.115 10770 Z= 0.375 Chirality : 0.044 0.218 1261 Planarity : 0.004 0.044 1356 Dihedral : 7.314 91.650 1147 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.36 % Favored : 92.54 % Rotamer: Outliers : 5.88 % Allowed : 23.66 % Favored : 70.45 % 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: -0.42 (0.27), residues: 1005 helix: 1.01 (0.31), residues: 267 sheet: -0.25 (0.30), residues: 303 loop : -1.05 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 304 HIS 0.010 0.002 HIS A 362 PHE 0.032 0.002 PHE G 6 TYR 0.021 0.002 TYR G 13 ARG 0.006 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 237 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 141 PHE cc_start: 0.7747 (m-80) cc_final: 0.7148 (m-80) REVERT: R 229 VAL cc_start: 0.8971 (t) cc_final: 0.8697 (p) REVERT: R 259 PRO cc_start: 0.8084 (Cg_endo) cc_final: 0.7827 (Cg_exo) REVERT: R 304 TRP cc_start: 0.8349 (OUTLIER) cc_final: 0.7827 (m-10) REVERT: R 352 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8425 (mm) REVERT: A 24 LYS cc_start: 0.9094 (pttm) cc_final: 0.8670 (pttm) REVERT: A 122 ASN cc_start: 0.8766 (t0) cc_final: 0.8496 (t0) REVERT: A 222 ASN cc_start: 0.8136 (t0) cc_final: 0.7309 (t0) REVERT: H 9 GLU cc_start: 0.8000 (pm20) cc_final: 0.7568 (pm20) REVERT: H 22 ARG cc_start: 0.7845 (ttp-170) cc_final: 0.7640 (ttp-170) REVERT: H 60 TYR cc_start: 0.7573 (m-10) cc_final: 0.7280 (m-10) REVERT: L 30 VAL cc_start: 0.8969 (t) cc_final: 0.8750 (m) REVERT: L 37 TYR cc_start: 0.8872 (m-80) cc_final: 0.8549 (m-80) REVERT: L 53 SER cc_start: 0.9068 (m) cc_final: 0.8687 (p) REVERT: L 83 ASP cc_start: 0.8302 (m-30) cc_final: 0.8016 (m-30) REVERT: L 91 GLN cc_start: 0.9079 (pp30) cc_final: 0.8495 (pp30) REVERT: B 63 VAL cc_start: 0.8477 (OUTLIER) cc_final: 0.8052 (p) REVERT: B 77 THR cc_start: 0.8022 (p) cc_final: 0.7791 (p) REVERT: B 96 ASN cc_start: 0.8737 (t0) cc_final: 0.8524 (t0) REVERT: B 109 GLN cc_start: 0.8320 (tm-30) cc_final: 0.8093 (tm-30) outliers start: 44 outliers final: 31 residues processed: 259 average time/residue: 0.2011 time to fit residues: 69.5245 Evaluate side-chains 268 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 234 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 152 SER Chi-restraints excluded: chain R residue 162 ILE Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 341 SER Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 15 VAL Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 27 optimal weight: 0.0980 chunk 81 optimal weight: 5.9990 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 298 ASN H 80 ASN B 3 GLN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7879 Z= 0.203 Angle : 0.695 11.571 10770 Z= 0.335 Chirality : 0.041 0.193 1261 Planarity : 0.004 0.046 1356 Dihedral : 7.037 89.492 1147 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.17 % Favored : 93.73 % Rotamer: Outliers : 5.35 % Allowed : 25.13 % Favored : 69.52 % 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: -0.34 (0.27), residues: 1005 helix: 1.19 (0.31), residues: 270 sheet: -0.15 (0.30), residues: 301 loop : -1.14 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 304 HIS 0.008 0.001 HIS A 362 PHE 0.029 0.001 PHE G 6 TYR 0.016 0.001 TYR R 239 ARG 0.003 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 241 time to evaluate : 0.877 Fit side-chains revert: symmetry clash REVERT: R 141 PHE cc_start: 0.7680 (m-80) cc_final: 0.7068 (m-80) REVERT: R 259 PRO cc_start: 0.8018 (Cg_endo) cc_final: 0.7745 (Cg_exo) REVERT: R 304 TRP cc_start: 0.8236 (OUTLIER) cc_final: 0.7909 (m-10) REVERT: R 352 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8368 (mm) REVERT: A 24 LYS cc_start: 0.9079 (pttm) cc_final: 0.8617 (pttm) REVERT: A 122 ASN cc_start: 0.8730 (t0) cc_final: 0.8459 (t0) REVERT: A 222 ASN cc_start: 0.8005 (t0) cc_final: 0.7180 (t0) REVERT: A 232 LYS cc_start: 0.8643 (tppp) cc_final: 0.8193 (tppp) REVERT: H 9 GLU cc_start: 0.7932 (pm20) cc_final: 0.7479 (pm20) REVERT: H 60 TYR cc_start: 0.7526 (m-10) cc_final: 0.7215 (m-10) REVERT: H 80 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8280 (t0) REVERT: L 53 SER cc_start: 0.9026 (m) cc_final: 0.8652 (p) REVERT: L 83 ASP cc_start: 0.8247 (m-30) cc_final: 0.7970 (m-30) REVERT: L 91 GLN cc_start: 0.8918 (pp30) cc_final: 0.8369 (pp30) REVERT: B 63 VAL cc_start: 0.8381 (OUTLIER) cc_final: 0.7924 (p) REVERT: B 77 THR cc_start: 0.7949 (p) cc_final: 0.7701 (p) outliers start: 40 outliers final: 28 residues processed: 261 average time/residue: 0.1931 time to fit residues: 67.5032 Evaluate side-chains 266 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 234 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 389 SER Chi-restraints excluded: chain R residue 394 LEU Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 368 HIS Chi-restraints excluded: chain H residue 80 ASN Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 39 GLN Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.0370 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 298 ASN H 80 ASN B 3 GLN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7879 Z= 0.201 Angle : 0.698 11.569 10770 Z= 0.335 Chirality : 0.041 0.195 1261 Planarity : 0.004 0.069 1356 Dihedral : 6.939 88.635 1147 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.27 % Favored : 93.63 % Rotamer: Outliers : 4.95 % Allowed : 25.13 % Favored : 69.92 % 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: -0.27 (0.27), residues: 1005 helix: 1.26 (0.31), residues: 269 sheet: -0.17 (0.30), residues: 304 loop : -1.05 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 304 HIS 0.008 0.001 HIS A 362 PHE 0.030 0.001 PHE G 6 TYR 0.013 0.001 TYR G 10 ARG 0.002 0.000 ARG L 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2010 Ramachandran restraints generated. 1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 247 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 141 PHE cc_start: 0.7660 (m-80) cc_final: 0.7029 (m-80) REVERT: R 229 VAL cc_start: 0.8953 (t) cc_final: 0.8682 (p) REVERT: R 259 PRO cc_start: 0.8001 (Cg_endo) cc_final: 0.7726 (Cg_exo) REVERT: R 304 TRP cc_start: 0.8268 (OUTLIER) cc_final: 0.7942 (m-10) REVERT: R 352 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 122 ASN cc_start: 0.8720 (t0) cc_final: 0.8445 (t0) REVERT: A 222 ASN cc_start: 0.7957 (t0) cc_final: 0.7122 (t0) REVERT: A 232 LYS cc_start: 0.8647 (tppp) cc_final: 0.8159 (tppp) REVERT: A 257 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7244 (mm-30) REVERT: H 9 GLU cc_start: 0.7884 (pm20) cc_final: 0.7411 (pm20) REVERT: H 60 TYR cc_start: 0.7521 (m-10) cc_final: 0.7213 (m-10) REVERT: H 90 ARG cc_start: 0.8467 (ptp-170) cc_final: 0.7940 (ptp90) REVERT: L 53 SER cc_start: 0.9030 (m) cc_final: 0.8644 (p) REVERT: L 83 ASP cc_start: 0.8182 (m-30) cc_final: 0.7903 (m-30) REVERT: L 91 GLN cc_start: 0.8841 (pp30) cc_final: 0.8295 (pp30) REVERT: B 63 VAL cc_start: 0.8350 (OUTLIER) cc_final: 0.7887 (p) REVERT: B 77 THR cc_start: 0.7901 (p) cc_final: 0.7670 (p) outliers start: 37 outliers final: 26 residues processed: 267 average time/residue: 0.1987 time to fit residues: 71.3137 Evaluate side-chains 276 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 247 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 149 TYR Chi-restraints excluded: chain R residue 226 VAL Chi-restraints excluded: chain R residue 247 LEU Chi-restraints excluded: chain R residue 252 LEU Chi-restraints excluded: chain R residue 304 TRP Chi-restraints excluded: chain R residue 329 LEU Chi-restraints excluded: chain R residue 352 LEU Chi-restraints excluded: chain R residue 424 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 111 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 243 LEU Chi-restraints excluded: chain A residue 244 PHE Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain L residue 20 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 55 LEU Chi-restraints excluded: chain L residue 73 THR Chi-restraints excluded: chain B residue 2 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 90 THR Chi-restraints excluded: chain B residue 111 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 7.9990 chunk 79 optimal weight: 0.0050 chunk 33 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 298 ASN ** A 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.086314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076140 restraints weight = 20439.999| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.91 r_work: 0.3070 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 7879 Z= 0.298 Angle : 0.724 10.270 10770 Z= 0.352 Chirality : 0.042 0.192 1261 Planarity : 0.004 0.066 1356 Dihedral : 7.072 89.425 1147 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.67 % Favored : 93.23 % Rotamer: Outliers : 4.68 % Allowed : 26.20 % Favored : 69.12 % 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: -0.37 (0.27), residues: 1005 helix: 1.18 (0.31), residues: 269 sheet: -0.25 (0.30), residues: 303 loop : -1.10 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 304 HIS 0.004 0.001 HIS A 219 PHE 0.029 0.002 PHE G 6 TYR 0.013 0.002 TYR H 107 ARG 0.003 0.000 ARG B 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2209.43 seconds wall clock time: 43 minutes 52.62 seconds (2632.62 seconds total)