Starting phenix.real_space_refine on Mon Mar 18 07:54:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/03_2024/8fhk_29087_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/03_2024/8fhk_29087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/03_2024/8fhk_29087.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/03_2024/8fhk_29087.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/03_2024/8fhk_29087_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fhk_29087/03_2024/8fhk_29087_trim_updated.pdb" } resolution = 2.9 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= 0.025 sd= 0.050 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: 7 Type Number sf(0) Gaussians P 19 5.49 5 Mg 2 5.21 5 S 40 5.16 5 C 6528 2.51 5 N 1652 2.21 5 O 1879 1.98 5 H 9827 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 19947 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 10395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 645, 10395 Classifications: {'peptide': 645} Link IDs: {'PTRANS': 13, 'TRANS': 631} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 9107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 574, 9107 Classifications: {'peptide': 574} Link IDs: {'PTRANS': 19, 'TRANS': 554} Chain: "D" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 297 Unusual residues: {' MG': 1, 'ATP': 1, 'POV': 11} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 343 Unresolved non-hydrogen dihedrals: 288 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'POV:plan-3': 6, 'POV:plan-2': 2, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 148 Unusual residues: {' MG': 1, 'ATP': 1, 'POV': 5} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 144 Unresolved non-hydrogen angles: 161 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 3, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 29 Time building chain proxies: 9.52, per 1000 atoms: 0.48 Number of scatterers: 19947 At special positions: 0 Unit cell: (74.405, 83.463, 158.515, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 40 16.00 P 19 15.00 Mg 2 11.99 O 1879 8.00 N 1652 7.00 C 6528 6.00 H 9827 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 17.16 Conformation dependent library (CDL) restraints added in 1.9 seconds 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2260 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 5 sheets defined 58.2% alpha, 3.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.31 Creating SS restraints... Processing helix chain 'D' and resid 3 through 12 Processing helix chain 'D' and resid 16 through 46 Proline residue: D 36 - end of helix removed outlier: 3.858A pdb=" N GLY D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASP D 45 " --> pdb=" O LYS D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 141 Processing helix chain 'D' and resid 144 through 195 removed outlier: 3.999A pdb=" N VAL D 161 " --> pdb=" O GLY D 157 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N PHE D 162 " --> pdb=" O GLY D 158 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE D 165 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET D 176 " --> pdb=" O TYR D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 202 Processing helix chain 'D' and resid 206 through 214 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 227 through 248 Processing helix chain 'D' and resid 252 through 272 removed outlier: 3.933A pdb=" N VAL D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) Proline residue: D 261 - end of helix Processing helix chain 'D' and resid 275 through 297 Processing helix chain 'D' and resid 299 through 305 Processing helix chain 'D' and resid 308 through 327 Processing helix chain 'D' and resid 337 through 360 removed outlier: 4.106A pdb=" N VAL D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ILE D 344 " --> pdb=" O LEU D 340 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE D 356 " --> pdb=" O LEU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 410 removed outlier: 3.503A pdb=" N PHE D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N GLN D 384 " --> pdb=" O ASN D 380 " (cutoff:3.500A) Proline residue: D 385 - end of helix removed outlier: 3.997A pdb=" N GLN D 392 " --> pdb=" O GLY D 388 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS D 395 " --> pdb=" O ASN D 391 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N VAL D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 439 through 441 No H-bonds generated for 'chain 'D' and resid 439 through 441' Processing helix chain 'D' and resid 469 through 476 Processing helix chain 'D' and resid 494 through 496 No H-bonds generated for 'chain 'D' and resid 494 through 496' Processing helix chain 'D' and resid 499 through 504 Processing helix chain 'D' and resid 520 through 525 Processing helix chain 'D' and resid 533 through 542 removed outlier: 3.748A pdb=" N ILE D 536 " --> pdb=" O GLU D 533 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LYS D 537 " --> pdb=" O GLU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 549 No H-bonds generated for 'chain 'D' and resid 546 through 549' Processing helix chain 'D' and resid 569 through 582 Processing helix chain 'D' and resid 600 through 603 No H-bonds generated for 'chain 'D' and resid 600 through 603' Processing helix chain 'D' and resid 605 through 608 No H-bonds generated for 'chain 'D' and resid 605 through 608' Processing helix chain 'D' and resid 625 through 628 Processing helix chain 'D' and resid 638 through 640 No H-bonds generated for 'chain 'D' and resid 638 through 640' Processing helix chain 'D' and resid 654 through 662 removed outlier: 3.598A pdb=" N TYR D 658 " --> pdb=" O LEU D 654 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 14 removed outlier: 5.162A pdb=" N TRP C 10 " --> pdb=" O LYS C 6 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N PHE C 11 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 12 " --> pdb=" O LEU C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 32 removed outlier: 3.542A pdb=" N VAL C 24 " --> pdb=" O THR C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 49 Processing helix chain 'C' and resid 54 through 101 removed outlier: 4.179A pdb=" N TRP C 78 " --> pdb=" O MET C 74 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 108 No H-bonds generated for 'chain 'C' and resid 106 through 108' Processing helix chain 'C' and resid 114 through 156 removed outlier: 4.258A pdb=" N ASP C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ILE C 136 " --> pdb=" O THR C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 206 removed outlier: 4.331A pdb=" N GLU C 185 " --> pdb=" O SER C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 214 removed outlier: 3.719A pdb=" N TYR C 214 " --> pdb=" O VAL C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 269 removed outlier: 3.844A pdb=" N ARG C 223 " --> pdb=" O ASN C 219 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 241 " --> pdb=" O LYS C 237 " (cutoff:3.500A) Proline residue: C 247 - end of helix Processing helix chain 'C' and resid 275 through 316 removed outlier: 3.612A pdb=" N TRP C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 5.353A pdb=" N ALA C 294 " --> pdb=" O TRP C 290 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLY C 296 " --> pdb=" O MET C 292 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N GLU C 297 " --> pdb=" O PHE C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 385 Processing helix chain 'C' and resid 407 through 413 Processing helix chain 'C' and resid 428 through 432 Processing helix chain 'C' and resid 443 through 450 Processing helix chain 'C' and resid 455 through 459 Processing helix chain 'C' and resid 477 through 489 Processing helix chain 'C' and resid 507 through 520 Processing helix chain 'C' and resid 535 through 537 No H-bonds generated for 'chain 'C' and resid 535 through 537' Processing helix chain 'C' and resid 558 through 561 No H-bonds generated for 'chain 'C' and resid 558 through 561' Processing helix chain 'C' and resid 565 through 575 removed outlier: 4.073A pdb=" N GLU C 571 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG C 572 " --> pdb=" O GLU C 568 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 89 through 93 Processing sheet with id= B, first strand: chain 'D' and resid 458 through 460 removed outlier: 6.312A pdb=" N GLN D 633 " --> pdb=" O VAL D 459 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'D' and resid 506 through 509 removed outlier: 6.519A pdb=" N ILE D 587 " --> pdb=" O GLY D 507 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N VAL D 509 " --> pdb=" O ILE D 587 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE D 589 " --> pdb=" O VAL D 509 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N THR D 617 " --> pdb=" O LEU D 588 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N LEU D 590 " --> pdb=" O THR D 617 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N PHE D 619 " --> pdb=" O LEU D 590 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'C' and resid 367 through 369 removed outlier: 7.152A pdb=" N LEU C 541 " --> pdb=" O GLY C 368 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU C 552 " --> pdb=" O VAL C 544 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ASP C 546 " --> pdb=" O ILE C 550 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ILE C 550 " --> pdb=" O ASP C 546 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 496 through 499 486 hydrogen bonds defined for protein. 1428 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: 7.68 Time building geometry restraints manager: 17.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.86 - 1.06: 3231 1.06 - 1.25: 8189 1.25 - 1.45: 2808 1.45 - 1.65: 5814 1.65 - 1.85: 80 Bond restraints: 20122 Sorted by residual: bond pdb=" NE1 TRP C 78 " pdb=" HE1 TRP C 78 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP D 54 " pdb=" HE1 TRP D 54 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.24e+02 bond pdb=" NE1 TRP C 10 " pdb=" HE1 TRP C 10 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 290 " pdb=" HE1 TRP C 290 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 bond pdb=" NE1 TRP C 565 " pdb=" HE1 TRP C 565 " ideal model delta sigma weight residual 0.860 1.082 -0.222 2.00e-02 2.50e+03 1.23e+02 ... (remaining 20117 not shown) Histogram of bond angle deviations from ideal: 94.37 - 111.35: 21883 111.35 - 128.34: 14187 128.34 - 145.32: 72 145.32 - 162.31: 1 162.31 - 179.29: 1 Bond angle restraints: 36144 Sorted by residual: angle pdb=" CA GLY D 108 " pdb=" N GLY D 108 " pdb=" H GLY D 108 " ideal model delta sigma weight residual 114.00 179.29 -65.29 3.00e+00 1.11e-01 4.74e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 122.12 14.71 1.00e+00 1.00e+00 2.16e+02 angle pdb=" O2G ATP C 601 " pdb=" PG ATP C 601 " pdb=" O3B ATP C 601 " ideal model delta sigma weight residual 104.48 118.62 -14.14 1.14e+00 7.76e-01 1.55e+02 angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 128.40 11.47 1.00e+00 1.00e+00 1.32e+02 angle pdb=" CA ALA D 64 " pdb=" N ALA D 64 " pdb=" H ALA D 64 " ideal model delta sigma weight residual 114.00 145.63 -31.63 3.00e+00 1.11e-01 1.11e+02 ... (remaining 36139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 9146 35.94 - 71.88: 334 71.88 - 107.82: 28 107.82 - 143.76: 6 143.76 - 179.70: 4 Dihedral angle restraints: 9518 sinusoidal: 5328 harmonic: 4190 Sorted by residual: dihedral pdb=" CA GLU D 80 " pdb=" C GLU D 80 " pdb=" N PRO D 81 " pdb=" CA PRO D 81 " ideal model delta harmonic sigma weight residual 180.00 153.07 26.93 0 5.00e+00 4.00e-02 2.90e+01 dihedral pdb=" C29 POV D 711 " pdb="C210 POV D 711 " pdb="C211 POV D 711 " pdb="C212 POV D 711 " ideal model delta sinusoidal sigma weight residual 112.25 -68.05 -179.70 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C27 POV D 705 " pdb=" C28 POV D 705 " pdb=" C29 POV D 705 " pdb="C210 POV D 705 " ideal model delta sinusoidal sigma weight residual 127.48 -61.85 -170.67 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 9515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1290 0.071 - 0.141: 196 0.141 - 0.212: 38 0.212 - 0.283: 7 0.283 - 0.353: 3 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CA VAL C 215 " pdb=" N VAL C 215 " pdb=" C VAL C 215 " pdb=" CB VAL C 215 " both_signs ideal model delta sigma weight residual False 2.44 2.09 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA ILE D 236 " pdb=" N ILE D 236 " pdb=" C ILE D 236 " pdb=" CB ILE D 236 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA ILE D 369 " pdb=" N ILE D 369 " pdb=" C ILE D 369 " pdb=" CB ILE D 369 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 1531 not shown) Planarity restraints: 2896 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D 706 " -0.212 2.00e-02 2.50e+03 2.59e-01 6.70e+02 pdb=" C29 POV D 706 " 0.432 2.00e-02 2.50e+03 pdb="C210 POV D 706 " -0.187 2.00e-02 2.50e+03 pdb="C211 POV D 706 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV C 605 " -0.079 2.00e-02 2.50e+03 2.55e-01 6.48e+02 pdb=" C29 POV C 605 " 0.321 2.00e-02 2.50e+03 pdb="C210 POV C 605 " -0.367 2.00e-02 2.50e+03 pdb="C211 POV C 605 " 0.125 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV D 704 " 0.098 2.00e-02 2.50e+03 2.35e-01 5.54e+02 pdb=" C29 POV D 704 " -0.315 2.00e-02 2.50e+03 pdb="C210 POV D 704 " 0.320 2.00e-02 2.50e+03 pdb="C211 POV D 704 " -0.103 2.00e-02 2.50e+03 ... (remaining 2893 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.10: 971 2.10 - 2.72: 33216 2.72 - 3.35: 57736 3.35 - 3.97: 77131 3.97 - 4.60: 116616 Nonbonded interactions: 285670 Sorted by model distance: nonbonded pdb=" HB1 ALA D 244 " pdb=" HH TYR D 378 " model vdw 1.469 2.270 nonbonded pdb=" HA3 GLY D 428 " pdb=" HG1 THR D 617 " model vdw 1.526 2.270 nonbonded pdb="HG13 VAL D 612 " pdb=" HG1 THR D 618 " model vdw 1.537 2.270 nonbonded pdb=" HG1 THR C 131 " pdb=" HA3 GLY C 305 " model vdw 1.565 2.270 nonbonded pdb=" HB2 HIS C 421 " pdb=" HZ2 LYS C 480 " model vdw 1.570 2.270 ... (remaining 285665 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: 6.490 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: 0.290 Extract box with map and model: 23.490 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 68.010 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 111.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 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 : 0.008 0.156 10295 Z= 0.553 Angle : 1.175 16.977 13872 Z= 0.764 Chirality : 0.057 0.353 1534 Planarity : 0.016 0.259 1716 Dihedral : 18.883 179.695 3961 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.39 % Allowed : 2.90 % Favored : 96.71 % 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: -1.60 (0.24), residues: 1207 helix: -0.13 (0.19), residues: 756 sheet: -1.62 (0.62), residues: 62 loop : -2.76 (0.28), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 290 HIS 0.007 0.001 HIS D 192 PHE 0.026 0.002 PHE D 254 TYR 0.019 0.002 TYR C 76 ARG 0.011 0.001 ARG C 411 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 185 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 181 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 144 MET cc_start: 0.6242 (ppp) cc_final: 0.6008 (tmt) REVERT: C 420 ASP cc_start: 0.7079 (m-30) cc_final: 0.6867 (m-30) outliers start: 4 outliers final: 3 residues processed: 183 average time/residue: 2.0235 time to fit residues: 406.1475 Evaluate side-chains 128 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 416 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 216 GLN C 458 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10295 Z= 0.218 Angle : 0.606 6.156 13872 Z= 0.324 Chirality : 0.039 0.161 1534 Planarity : 0.005 0.083 1716 Dihedral : 17.723 176.194 1667 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 1.74 % Allowed : 12.28 % Favored : 85.98 % 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: -1.12 (0.24), residues: 1207 helix: 0.23 (0.19), residues: 760 sheet: -1.03 (0.69), residues: 52 loop : -2.60 (0.28), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 290 HIS 0.004 0.001 HIS D 192 PHE 0.017 0.002 PHE C 108 TYR 0.017 0.001 TYR C 109 ARG 0.006 0.001 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 133 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 86 LYS cc_start: 0.3841 (mptt) cc_final: 0.3557 (mptt) REVERT: D 159 LEU cc_start: 0.6619 (tm) cc_final: 0.6371 (tp) REVERT: D 297 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7810 (mm-40) REVERT: C 108 PHE cc_start: 0.6937 (OUTLIER) cc_final: 0.6722 (t80) REVERT: C 358 SER cc_start: 0.7894 (m) cc_final: 0.7341 (t) REVERT: C 420 ASP cc_start: 0.7244 (m-30) cc_final: 0.7043 (m-30) outliers start: 18 outliers final: 6 residues processed: 144 average time/residue: 1.8608 time to fit residues: 296.2641 Evaluate side-chains 127 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 120 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 108 PHE Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 458 HIS Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 458 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6899 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10295 Z= 0.248 Angle : 0.592 6.345 13872 Z= 0.325 Chirality : 0.039 0.151 1534 Planarity : 0.005 0.065 1716 Dihedral : 16.676 164.021 1665 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 1.93 % Allowed : 13.35 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1207 helix: 0.20 (0.19), residues: 758 sheet: -0.95 (0.69), residues: 52 loop : -2.48 (0.29), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 290 HIS 0.015 0.001 HIS C 458 PHE 0.016 0.002 PHE C 155 TYR 0.017 0.002 TYR C 19 ARG 0.005 0.001 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.457 Fit side-chains TARDY: cannot create tardy model for: "TYR D 142 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 38 ILE cc_start: 0.7574 (mp) cc_final: 0.7365 (mp) REVERT: D 86 LYS cc_start: 0.3919 (mptt) cc_final: 0.3668 (mptt) REVERT: D 159 LEU cc_start: 0.6694 (tm) cc_final: 0.6440 (tp) REVERT: C 8 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6694 (mp) REVERT: C 358 SER cc_start: 0.7963 (m) cc_final: 0.7465 (t) REVERT: C 458 HIS cc_start: 0.5998 (OUTLIER) cc_final: 0.5496 (m90) outliers start: 20 outliers final: 10 residues processed: 142 average time/residue: 1.8678 time to fit residues: 294.2937 Evaluate side-chains 136 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 538 ASN Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 458 HIS Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 57 optimal weight: 6.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 10295 Z= 0.406 Angle : 0.703 7.609 13872 Z= 0.385 Chirality : 0.043 0.153 1534 Planarity : 0.006 0.061 1716 Dihedral : 16.472 113.415 1663 Min Nonbonded Distance : 1.669 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.37 % Favored : 91.55 % Rotamer: Outliers : 3.29 % Allowed : 13.73 % Favored : 82.98 % 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: -1.93 (0.22), residues: 1207 helix: -0.61 (0.18), residues: 758 sheet: -0.73 (0.72), residues: 47 loop : -2.52 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP C 290 HIS 0.010 0.002 HIS D 322 PHE 0.022 0.003 PHE D 315 TYR 0.021 0.003 TYR C 19 ARG 0.012 0.001 ARG C 120 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 125 time to evaluate : 1.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 159 LEU cc_start: 0.6763 (tm) cc_final: 0.6560 (tp) REVERT: C 273 LEU cc_start: 0.7401 (OUTLIER) cc_final: 0.7054 (tt) outliers start: 34 outliers final: 14 residues processed: 143 average time/residue: 1.9039 time to fit residues: 302.2910 Evaluate side-chains 129 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 459 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 80 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 104 optimal weight: 0.3980 chunk 29 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 ASN C 458 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10295 Z= 0.204 Angle : 0.578 6.743 13872 Z= 0.312 Chirality : 0.039 0.167 1534 Planarity : 0.005 0.053 1716 Dihedral : 15.282 89.697 1663 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.46 % Favored : 92.46 % Rotamer: Outliers : 2.90 % Allowed : 14.89 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.24), residues: 1207 helix: -0.02 (0.19), residues: 759 sheet: -0.62 (0.70), residues: 52 loop : -2.48 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 290 HIS 0.006 0.001 HIS C 458 PHE 0.027 0.002 PHE D 315 TYR 0.017 0.002 TYR C 19 ARG 0.005 0.000 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 1.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 259 ILE cc_start: 0.5354 (OUTLIER) cc_final: 0.4955 (mp) REVERT: C 166 ILE cc_start: 0.7778 (OUTLIER) cc_final: 0.7395 (mp) REVERT: C 273 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6962 (tt) REVERT: C 500 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7712 (mp10) REVERT: C 538 HIS cc_start: 0.6484 (p-80) cc_final: 0.6240 (p-80) outliers start: 30 outliers final: 15 residues processed: 145 average time/residue: 1.9036 time to fit residues: 306.1918 Evaluate side-chains 133 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 42 MET Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 458 HIS Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 458 HIS C 500 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 10295 Z= 0.338 Angle : 0.633 6.929 13872 Z= 0.348 Chirality : 0.041 0.153 1534 Planarity : 0.005 0.055 1716 Dihedral : 15.552 99.999 1663 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.95 % Favored : 91.96 % Rotamer: Outliers : 2.71 % Allowed : 16.34 % Favored : 80.95 % 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: -1.63 (0.23), residues: 1207 helix: -0.33 (0.18), residues: 758 sheet: -0.24 (0.82), residues: 42 loop : -2.53 (0.28), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 290 HIS 0.021 0.002 HIS C 458 PHE 0.023 0.002 PHE D 315 TYR 0.019 0.002 TYR C 19 ARG 0.005 0.001 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 118 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 347 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7525 (mm) REVERT: C 166 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7409 (mp) REVERT: C 273 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7091 (tt) outliers start: 28 outliers final: 17 residues processed: 137 average time/residue: 1.8816 time to fit residues: 287.0636 Evaluate side-chains 133 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 113 time to evaluate : 1.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 342 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10295 Z= 0.252 Angle : 0.596 6.516 13872 Z= 0.325 Chirality : 0.039 0.187 1534 Planarity : 0.005 0.057 1716 Dihedral : 15.160 90.274 1663 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.12 % Favored : 91.80 % Rotamer: Outliers : 2.71 % Allowed : 16.92 % Favored : 80.37 % 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: -1.45 (0.24), residues: 1207 helix: -0.19 (0.18), residues: 764 sheet: -0.33 (0.76), residues: 52 loop : -2.52 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 290 HIS 0.008 0.001 HIS C 458 PHE 0.025 0.002 PHE D 315 TYR 0.017 0.002 TYR C 19 ARG 0.010 0.000 ARG C 362 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 151 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 123 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 347 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7536 (mm) REVERT: C 146 MET cc_start: 0.6806 (OUTLIER) cc_final: 0.5181 (mpt) REVERT: C 166 ILE cc_start: 0.7786 (OUTLIER) cc_final: 0.7376 (mp) REVERT: C 273 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7070 (tt) REVERT: C 538 HIS cc_start: 0.6545 (p-80) cc_final: 0.6302 (p-80) outliers start: 28 outliers final: 16 residues processed: 144 average time/residue: 1.9810 time to fit residues: 313.9931 Evaluate side-chains 136 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 chunk 106 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10295 Z= 0.192 Angle : 0.564 6.643 13872 Z= 0.304 Chirality : 0.038 0.160 1534 Planarity : 0.005 0.063 1716 Dihedral : 14.484 86.412 1663 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.04 % Favored : 91.88 % Rotamer: Outliers : 2.13 % Allowed : 17.89 % Favored : 79.98 % 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: -1.10 (0.24), residues: 1207 helix: 0.12 (0.19), residues: 764 sheet: -0.26 (0.75), residues: 52 loop : -2.46 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 290 HIS 0.007 0.001 HIS C 458 PHE 0.028 0.001 PHE D 315 TYR 0.014 0.001 TYR C 19 ARG 0.012 0.000 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 146 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 124 time to evaluate : 1.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.7805 (pptt) cc_final: 0.7128 (mtpm) REVERT: D 347 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7561 (mm) REVERT: D 375 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7556 (t80) REVERT: C 166 ILE cc_start: 0.7818 (OUTLIER) cc_final: 0.7611 (mp) REVERT: C 273 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.7030 (tt) REVERT: C 538 HIS cc_start: 0.6513 (p-80) cc_final: 0.6286 (p-80) outliers start: 22 outliers final: 15 residues processed: 138 average time/residue: 1.9203 time to fit residues: 294.0175 Evaluate side-chains 133 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 267 SER Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 108 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 114 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10295 Z= 0.207 Angle : 0.565 6.616 13872 Z= 0.306 Chirality : 0.038 0.169 1534 Planarity : 0.005 0.062 1716 Dihedral : 14.255 86.095 1663 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.20 % Favored : 91.71 % Rotamer: Outliers : 2.32 % Allowed : 18.18 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.24), residues: 1207 helix: 0.19 (0.19), residues: 764 sheet: -0.38 (0.73), residues: 52 loop : -2.46 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 290 HIS 0.005 0.001 HIS C 458 PHE 0.015 0.001 PHE D 315 TYR 0.023 0.002 TYR D 98 ARG 0.015 0.000 ARG D 624 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 144 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 120 time to evaluate : 1.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 135 LYS cc_start: 0.7819 (pptt) cc_final: 0.7146 (mtpm) REVERT: D 347 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7567 (mm) REVERT: D 375 PHE cc_start: 0.7836 (OUTLIER) cc_final: 0.7475 (t80) REVERT: C 8 LEU cc_start: 0.7009 (OUTLIER) cc_final: 0.6763 (mp) REVERT: C 273 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.7068 (tt) REVERT: C 538 HIS cc_start: 0.6516 (p-80) cc_final: 0.6281 (p-80) outliers start: 24 outliers final: 15 residues processed: 137 average time/residue: 1.7896 time to fit residues: 272.5286 Evaluate side-chains 133 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 461 LEU Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10295 Z= 0.207 Angle : 0.569 6.899 13872 Z= 0.306 Chirality : 0.038 0.153 1534 Planarity : 0.005 0.065 1716 Dihedral : 14.079 89.197 1663 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.95 % Favored : 91.96 % Rotamer: Outliers : 1.74 % Allowed : 19.05 % Favored : 79.21 % 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: -1.01 (0.24), residues: 1207 helix: 0.21 (0.19), residues: 765 sheet: -0.46 (0.73), residues: 52 loop : -2.44 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 290 HIS 0.005 0.001 HIS C 458 PHE 0.028 0.002 PHE D 315 TYR 0.015 0.002 TYR C 19 ARG 0.017 0.001 ARG D 624 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2414 Ramachandran restraints generated. 1207 Oldfield, 0 Emsley, 1207 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ILE 262 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 185 MET cc_start: 0.6715 (ttp) cc_final: 0.6479 (ttp) REVERT: D 336 MET cc_start: 0.6239 (mmt) cc_final: 0.5501 (mmt) REVERT: D 347 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7579 (mm) REVERT: D 375 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7590 (t80) REVERT: C 8 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6770 (mp) REVERT: C 273 LEU cc_start: 0.7395 (OUTLIER) cc_final: 0.7064 (tt) REVERT: C 538 HIS cc_start: 0.6522 (p-80) cc_final: 0.6293 (p-80) outliers start: 18 outliers final: 14 residues processed: 130 average time/residue: 1.8581 time to fit residues: 268.3025 Evaluate side-chains 134 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 116 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 338 HIS Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain D residue 375 PHE Chi-restraints excluded: chain D residue 473 LEU Chi-restraints excluded: chain D residue 599 THR Chi-restraints excluded: chain D residue 625 LEU Chi-restraints excluded: chain C residue 8 LEU Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 396 THR Chi-restraints excluded: chain C residue 416 TYR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 550 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 84 optimal weight: 0.0000 chunk 5 optimal weight: 6.9990 chunk 69 optimal weight: 2.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 606 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.109921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.098116 restraints weight = 64744.563| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.89 r_work: 0.3931 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3807 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10295 Z= 0.172 Angle : 0.551 6.608 13872 Z= 0.296 Chirality : 0.038 0.159 1534 Planarity : 0.005 0.064 1716 Dihedral : 13.319 85.434 1663 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.29 % Favored : 92.63 % Rotamer: Outliers : 1.64 % Allowed : 18.96 % Favored : 79.40 % 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: -0.77 (0.24), residues: 1207 helix: 0.44 (0.19), residues: 764 sheet: -0.27 (0.74), residues: 52 loop : -2.45 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 78 HIS 0.005 0.001 HIS C 458 PHE 0.021 0.001 PHE D 315 TYR 0.014 0.001 TYR C 19 ARG 0.016 0.000 ARG D 624 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6798.05 seconds wall clock time: 120 minutes 15.00 seconds (7215.00 seconds total)