Starting phenix.real_space_refine on Fri Mar 15 16:22:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/03_2024/7zrd_14911_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/03_2024/7zrd_14911.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/03_2024/7zrd_14911.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/03_2024/7zrd_14911.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/03_2024/7zrd_14911_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zrd_14911/03_2024/7zrd_14911_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= 0.000 sd= 0.006 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 1080 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: 7 Type Number sf(0) Gaussians K 9 8.98 5 V 1 8.30 5 P 5 5.49 5 S 62 5.16 5 C 7135 2.51 5 N 1823 2.21 5 O 2002 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 27": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 509": "OE1" <-> "OE2" Residue "B ASP 552": "OD1" <-> "OD2" Residue "B PHE 578": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 11037 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 216 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5021 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 26, 'TRANS': 649} Chain: "A" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 207 Unusual residues: {' K': 7, 'CDL': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "B" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 7 Unusual residues: {' K': 2, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.43, per 1000 atoms: 0.58 Number of scatterers: 11037 At special positions: 0 Unit cell: (88.044, 112.332, 142.692, 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) V 1 22.97 K 9 19.00 S 62 16.00 P 5 15.00 O 2002 8.00 N 1823 7.00 C 7135 6.00 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: 4.54 Conformation dependent library (CDL) restraints added in 2.2 seconds 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2642 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 56 helices and 6 sheets defined 55.9% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 31 Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 42 through 50 Processing helix chain 'A' and resid 59 through 82 Processing helix chain 'A' and resid 84 through 86 No H-bonds generated for 'chain 'A' and resid 84 through 86' Processing helix chain 'A' and resid 99 through 110 Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 126 through 131 Processing helix chain 'A' and resid 133 through 156 removed outlier: 3.662A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 176 Processing helix chain 'A' and resid 178 through 191 removed outlier: 3.612A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.769A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 273 removed outlier: 4.398A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 277 through 303 removed outlier: 3.595A pdb=" N LEU A 283 " --> pdb=" O GLN A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.704A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 380 through 398 Processing helix chain 'A' and resid 411 through 436 removed outlier: 4.633A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 449 through 464 removed outlier: 3.552A pdb=" N ALA A 464 " --> pdb=" O SER A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 494 Processing helix chain 'A' and resid 497 through 507 Processing helix chain 'A' and resid 524 through 549 Proline residue: A 545 - end of helix Processing helix chain 'A' and resid 551 through 556 Processing helix chain 'C' and resid 4 through 20 Processing helix chain 'C' and resid 22 through 33 Processing helix chain 'C' and resid 92 through 108 Processing helix chain 'C' and resid 134 through 139 Processing helix chain 'C' and resid 141 through 148 Processing helix chain 'C' and resid 152 through 161 Processing helix chain 'C' and resid 178 through 189 removed outlier: 3.601A pdb=" N ASP C 189 " --> pdb=" O LEU C 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 24 Processing helix chain 'B' and resid 12 through 19 removed outlier: 4.000A pdb=" N GLN B 16 " --> pdb=" O THR B 12 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ALA B 17 " --> pdb=" O LEU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 55 Processing helix chain 'B' and resid 64 through 101 removed outlier: 3.609A pdb=" N GLU B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLN B 93 " --> pdb=" O ARG B 89 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ALA B 94 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 159 No H-bonds generated for 'chain 'B' and resid 156 through 159' Processing helix chain 'B' and resid 171 through 173 No H-bonds generated for 'chain 'B' and resid 171 through 173' Processing helix chain 'B' and resid 199 through 208 Processing helix chain 'B' and resid 216 through 246 removed outlier: 3.946A pdb=" N TRP B 240 " --> pdb=" O THR B 236 " (cutoff:3.500A) Proline residue: B 241 - end of helix removed outlier: 3.946A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 262 Processing helix chain 'B' and resid 265 through 284 removed outlier: 5.871A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 300 removed outlier: 3.719A pdb=" N GLY B 299 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ASP B 300 " --> pdb=" O GLU B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 341 Processing helix chain 'B' and resid 347 through 360 removed outlier: 3.726A pdb=" N VAL B 353 " --> pdb=" O GLY B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 407 Processing helix chain 'B' and resid 417 through 426 Processing helix chain 'B' and resid 453 through 462 Processing helix chain 'B' and resid 475 through 485 removed outlier: 3.655A pdb=" N ALA B 480 " --> pdb=" O LEU B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 508 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 539 through 542 No H-bonds generated for 'chain 'B' and resid 539 through 542' Processing helix chain 'B' and resid 555 through 594 removed outlier: 4.148A pdb=" N LEU B 558 " --> pdb=" O PRO B 555 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS B 566 " --> pdb=" O HIS B 563 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET B 570 " --> pdb=" O GLN B 567 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU B 575 " --> pdb=" O ARG B 572 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN B 582 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL B 584 " --> pdb=" O ALA B 581 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ILE B 591 " --> pdb=" O PHE B 588 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 600 through 605 removed outlier: 3.805A pdb=" N ASN B 603 " --> pdb=" O PRO B 600 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 637 removed outlier: 4.152A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Proline residue: B 633 - end of helix Processing helix chain 'B' and resid 646 through 679 removed outlier: 4.231A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLY B 660 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 202 through 205 Processing sheet with id= B, first strand: chain 'B' and resid 131 through 134 removed outlier: 3.631A pdb=" N LEU B 187 " --> pdb=" O VAL B 134 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL B 188 " --> pdb=" O GLU B 148 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU B 148 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N GLU B 190 " --> pdb=" O VAL B 146 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N VAL B 146 " --> pdb=" O GLU B 190 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.556A pdb=" N ALA B 151 " --> pdb=" O ARG B 167 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG B 167 " --> pdb=" O ALA B 151 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 548 through 550 removed outlier: 3.653A pdb=" N VAL B 531 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.290A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LYS B 466 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ASP B 489 " --> pdb=" O MET B 469 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 373 through 375 removed outlier: 3.577A pdb=" N GLY B 385 " --> pdb=" O VAL B 375 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 393 through 397 removed outlier: 3.907A pdb=" N THR B 429 " --> pdb=" O LEU B 445 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL B 433 " --> pdb=" O GLY B 441 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N GLY B 441 " --> pdb=" O VAL B 433 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N GLU B 435 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 439 " --> pdb=" O GLU B 435 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 444 " --> pdb=" O GLU B 321 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLU B 321 " --> pdb=" O ALA B 444 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LYS B 446 " --> pdb=" O ALA B 319 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA B 319 " --> pdb=" O LYS B 446 " (cutoff:3.500A) 555 hydrogen bonds defined for protein. 1536 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: 3.22 Time building geometry restraints manager: 4.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3520 1.34 - 1.49: 2621 1.49 - 1.63: 4969 1.63 - 1.77: 1 1.77 - 1.91: 115 Bond restraints: 11226 Sorted by residual: bond pdb=" OA3 CDL A 609 " pdb=" PA1 CDL A 609 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.78e+00 bond pdb=" OB3 CDL A 608 " pdb=" PB2 CDL A 608 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.77e+00 bond pdb=" OB3 CDL A 609 " pdb=" PB2 CDL A 609 " ideal model delta sigma weight residual 1.529 1.503 0.026 1.00e-02 1.00e+04 6.51e+00 bond pdb=" OA3 CDL A 608 " pdb=" PA1 CDL A 608 " ideal model delta sigma weight residual 1.529 1.504 0.025 1.00e-02 1.00e+04 6.38e+00 bond pdb=" C11 CDL A 608 " pdb=" C12 CDL A 608 " ideal model delta sigma weight residual 1.523 1.492 0.031 1.50e-02 4.44e+03 4.29e+00 ... (remaining 11221 not shown) Histogram of bond angle deviations from ideal: 97.06 - 104.48: 210 104.48 - 111.89: 5390 111.89 - 119.31: 4075 119.31 - 126.72: 5400 126.72 - 134.14: 158 Bond angle restraints: 15233 Sorted by residual: angle pdb=" C LEU A 261 " pdb=" N ILE A 262 " pdb=" CA ILE A 262 " ideal model delta sigma weight residual 120.24 122.82 -2.58 6.30e-01 2.52e+00 1.68e+01 angle pdb=" C PRO C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta sigma weight residual 121.54 128.78 -7.24 1.91e+00 2.74e-01 1.44e+01 angle pdb=" C ASN B 547 " pdb=" N MET B 548 " pdb=" CA MET B 548 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" N VAL B 664 " pdb=" CA VAL B 664 " pdb=" C VAL B 664 " ideal model delta sigma weight residual 108.88 116.65 -7.77 2.16e+00 2.14e-01 1.29e+01 angle pdb=" C ALA B 210 " pdb=" N GLN B 211 " pdb=" CA GLN B 211 " ideal model delta sigma weight residual 122.08 127.11 -5.03 1.47e+00 4.63e-01 1.17e+01 ... (remaining 15228 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 5893 17.41 - 34.82: 631 34.82 - 52.22: 166 52.22 - 69.63: 41 69.63 - 87.04: 12 Dihedral angle restraints: 6743 sinusoidal: 2631 harmonic: 4112 Sorted by residual: dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 156.74 23.26 0 5.00e+00 4.00e-02 2.16e+01 dihedral pdb=" CA LEU B 183 " pdb=" C LEU B 183 " pdb=" N SER B 184 " pdb=" CA SER B 184 " ideal model delta harmonic sigma weight residual 180.00 -159.15 -20.85 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA PHE C 34 " pdb=" C PHE C 34 " pdb=" N PRO C 35 " pdb=" CA PRO C 35 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 6740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1420 0.055 - 0.109: 331 0.109 - 0.164: 55 0.164 - 0.218: 5 0.218 - 0.273: 3 Chirality restraints: 1814 Sorted by residual: chirality pdb=" CB VAL B 664 " pdb=" CA VAL B 664 " pdb=" CG1 VAL B 664 " pdb=" CG2 VAL B 664 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL B 14 " pdb=" CA VAL B 14 " pdb=" CG1 VAL B 14 " pdb=" CG2 VAL B 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.53e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 1811 not shown) Planarity restraints: 1912 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 323 " 0.082 5.00e-02 4.00e+02 1.23e-01 2.42e+01 pdb=" N PRO B 324 " -0.213 5.00e-02 4.00e+02 pdb=" CA PRO B 324 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 324 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 429 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO B 430 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO B 430 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 430 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 361 " 0.035 5.00e-02 4.00e+02 5.20e-02 4.33e+00 pdb=" N PRO A 362 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 362 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 362 " 0.029 5.00e-02 4.00e+02 ... (remaining 1909 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.85: 3614 2.85 - 3.42: 12278 3.42 - 3.99: 21772 3.99 - 4.57: 30998 4.57 - 5.14: 44521 Nonbonded interactions: 113183 Sorted by model distance: nonbonded pdb=" OG SER B 615 " pdb=" OD1 ASP B 673 " model vdw 2.272 2.440 nonbonded pdb=" O TYR C 22 " pdb=" OG1 THR C 26 " model vdw 2.283 2.440 nonbonded pdb=" O GLN B 422 " pdb=" OE1 GLN B 426 " model vdw 2.283 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG1 THR A 123 " model vdw 2.284 2.440 nonbonded pdb=" OG SER A 462 " pdb=" O SER A 469 " model vdw 2.315 2.440 ... (remaining 113178 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 3.550 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 33.340 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11226 Z= 0.287 Angle : 0.809 10.413 15233 Z= 0.413 Chirality : 0.048 0.273 1814 Planarity : 0.006 0.123 1912 Dihedral : 16.186 87.042 4101 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: -0.83 (0.20), residues: 1441 helix: -0.14 (0.16), residues: 856 sheet: -0.24 (0.64), residues: 76 loop : -1.13 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 115 HIS 0.003 0.001 HIS A 242 PHE 0.027 0.002 PHE A 260 TYR 0.035 0.002 TYR A 555 ARG 0.015 0.000 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.228 Fit side-chains revert: symmetry clash REVERT: A 287 MET cc_start: 0.8426 (mtt) cc_final: 0.8179 (mtt) REVERT: A 383 MET cc_start: 0.8289 (tpp) cc_final: 0.7901 (tpt) REVERT: B 469 MET cc_start: 0.7216 (tmm) cc_final: 0.6963 (tmm) REVERT: B 490 PHE cc_start: 0.7425 (p90) cc_final: 0.7138 (p90) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2091 time to fit residues: 46.8557 Evaluate side-chains 122 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 112 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 129 optimal weight: 0.0670 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS B 217 ASN B 390 ASN ** B 426 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 624 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11226 Z= 0.206 Angle : 0.505 6.777 15233 Z= 0.257 Chirality : 0.039 0.145 1814 Planarity : 0.005 0.081 1912 Dihedral : 11.018 62.218 1717 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.14 % Allowed : 7.22 % Favored : 91.64 % 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: 0.20 (0.21), residues: 1441 helix: 0.85 (0.17), residues: 855 sheet: -0.14 (0.61), residues: 81 loop : -0.98 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 655 HIS 0.005 0.001 HIS A 451 PHE 0.017 0.001 PHE B 199 TYR 0.016 0.001 TYR A 381 ARG 0.003 0.000 ARG B 363 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.130 Fit side-chains REVERT: A 227 MET cc_start: 0.8246 (mmm) cc_final: 0.7860 (mmm) REVERT: A 383 MET cc_start: 0.8360 (tpp) cc_final: 0.7953 (tpt) REVERT: B 490 PHE cc_start: 0.7500 (p90) cc_final: 0.7179 (p90) outliers start: 13 outliers final: 11 residues processed: 137 average time/residue: 0.2139 time to fit residues: 43.3023 Evaluate side-chains 130 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain C residue 128 LEU Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 130 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 44 optimal weight: 0.0980 chunk 104 optimal weight: 4.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS B 217 ASN B 390 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11226 Z= 0.283 Angle : 0.533 7.094 15233 Z= 0.271 Chirality : 0.041 0.154 1814 Planarity : 0.004 0.064 1912 Dihedral : 10.612 64.169 1717 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.58 % Allowed : 9.51 % Favored : 88.91 % 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: 0.36 (0.22), residues: 1441 helix: 1.02 (0.18), residues: 850 sheet: -0.39 (0.59), residues: 83 loop : -0.90 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 71 HIS 0.006 0.001 HIS A 451 PHE 0.011 0.001 PHE A 260 TYR 0.019 0.002 TYR A 381 ARG 0.004 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.284 Fit side-chains REVERT: A 227 MET cc_start: 0.8335 (mmm) cc_final: 0.7995 (mmm) REVERT: A 383 MET cc_start: 0.8385 (tpp) cc_final: 0.7952 (tpt) REVERT: A 439 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7847 (t0) REVERT: A 445 MET cc_start: 0.7854 (mmm) cc_final: 0.7649 (mtt) REVERT: B 93 GLN cc_start: 0.6823 (OUTLIER) cc_final: 0.6555 (pt0) REVERT: B 490 PHE cc_start: 0.7556 (p90) cc_final: 0.7333 (p90) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 0.2136 time to fit residues: 41.2932 Evaluate side-chains 132 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 130 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 68 optimal weight: 0.0670 chunk 123 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.3524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 217 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11226 Z= 0.216 Angle : 0.489 7.050 15233 Z= 0.248 Chirality : 0.039 0.135 1814 Planarity : 0.004 0.056 1912 Dihedral : 10.350 61.315 1717 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.58 % Allowed : 11.27 % Favored : 87.15 % 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: 0.54 (0.22), residues: 1441 helix: 1.17 (0.18), residues: 850 sheet: -0.49 (0.58), residues: 83 loop : -0.81 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 PHE 0.010 0.001 PHE A 527 TYR 0.018 0.001 TYR A 381 ARG 0.002 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.050 Fit side-chains REVERT: A 227 MET cc_start: 0.8323 (mmm) cc_final: 0.7977 (mmm) REVERT: A 274 MET cc_start: 0.8036 (mmm) cc_final: 0.7775 (mmm) REVERT: A 383 MET cc_start: 0.8436 (tpp) cc_final: 0.8004 (tpt) REVERT: A 439 ASP cc_start: 0.8165 (OUTLIER) cc_final: 0.7854 (t0) REVERT: B 93 GLN cc_start: 0.6716 (OUTLIER) cc_final: 0.6429 (pt0) REVERT: B 490 PHE cc_start: 0.7585 (p90) cc_final: 0.7288 (p90) outliers start: 18 outliers final: 14 residues processed: 130 average time/residue: 0.2150 time to fit residues: 41.2620 Evaluate side-chains 131 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 7.9990 chunk 78 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 102 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 95 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 124 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11226 Z= 0.283 Angle : 0.523 7.140 15233 Z= 0.265 Chirality : 0.040 0.139 1814 Planarity : 0.004 0.053 1912 Dihedral : 10.156 59.784 1717 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.82 % Allowed : 11.80 % Favored : 85.39 % 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: 0.52 (0.22), residues: 1441 helix: 1.12 (0.18), residues: 852 sheet: -0.54 (0.57), residues: 83 loop : -0.74 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 115 HIS 0.004 0.001 HIS A 451 PHE 0.011 0.001 PHE A 109 TYR 0.019 0.002 TYR A 381 ARG 0.004 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 1.215 Fit side-chains REVERT: A 227 MET cc_start: 0.8412 (mmm) cc_final: 0.8083 (mmm) REVERT: A 274 MET cc_start: 0.8170 (mmm) cc_final: 0.7918 (mmm) REVERT: A 383 MET cc_start: 0.8413 (tpp) cc_final: 0.8000 (tpt) REVERT: A 439 ASP cc_start: 0.8235 (OUTLIER) cc_final: 0.7988 (t0) REVERT: B 93 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6497 (pt0) outliers start: 32 outliers final: 26 residues processed: 133 average time/residue: 0.2086 time to fit residues: 41.5707 Evaluate side-chains 140 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 112 time to evaluate : 1.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 437 MET Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 158 ILE Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 662 LEU Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.7980 chunk 124 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 0.2980 chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11226 Z= 0.153 Angle : 0.460 7.035 15233 Z= 0.234 Chirality : 0.038 0.131 1814 Planarity : 0.004 0.051 1912 Dihedral : 9.780 59.450 1717 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.38 % Allowed : 12.06 % Favored : 85.56 % 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: 0.85 (0.23), residues: 1441 helix: 1.43 (0.18), residues: 851 sheet: -0.48 (0.59), residues: 85 loop : -0.67 (0.28), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.002 0.000 HIS A 85 PHE 0.009 0.001 PHE A 527 TYR 0.017 0.001 TYR A 381 ARG 0.003 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.158 Fit side-chains revert: symmetry clash REVERT: A 274 MET cc_start: 0.8133 (mmm) cc_final: 0.7924 (mmm) REVERT: A 383 MET cc_start: 0.8411 (tpp) cc_final: 0.8001 (tpt) REVERT: A 439 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7963 (t0) REVERT: B 93 GLN cc_start: 0.6794 (OUTLIER) cc_final: 0.6366 (pt0) outliers start: 27 outliers final: 20 residues processed: 137 average time/residue: 0.2086 time to fit residues: 42.4826 Evaluate side-chains 135 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 0.0970 chunk 101 optimal weight: 0.7980 chunk 116 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 137 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 84 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11226 Z= 0.159 Angle : 0.469 7.049 15233 Z= 0.237 Chirality : 0.038 0.178 1814 Planarity : 0.004 0.047 1912 Dihedral : 9.587 59.856 1717 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.38 % Allowed : 12.85 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.23), residues: 1441 helix: 1.55 (0.18), residues: 851 sheet: -0.34 (0.60), residues: 83 loop : -0.62 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 115 HIS 0.002 0.000 HIS A 85 PHE 0.010 0.001 PHE A 527 TYR 0.016 0.001 TYR A 381 ARG 0.004 0.000 ARG B 359 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.188 Fit side-chains REVERT: A 227 MET cc_start: 0.8030 (mmm) cc_final: 0.7699 (mmm) REVERT: A 383 MET cc_start: 0.8416 (tpp) cc_final: 0.8003 (tpt) REVERT: A 439 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7986 (t0) REVERT: B 93 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6306 (pt0) outliers start: 27 outliers final: 22 residues processed: 131 average time/residue: 0.2495 time to fit residues: 48.6780 Evaluate side-chains 135 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 27 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 93 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 108 optimal weight: 7.9990 chunk 125 optimal weight: 8.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11226 Z= 0.161 Angle : 0.466 7.049 15233 Z= 0.234 Chirality : 0.038 0.162 1814 Planarity : 0.003 0.046 1912 Dihedral : 9.384 59.326 1717 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.38 % Allowed : 13.03 % Favored : 84.60 % 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 (0.23), residues: 1441 helix: 1.57 (0.18), residues: 852 sheet: -0.34 (0.61), residues: 83 loop : -0.60 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 115 HIS 0.002 0.000 HIS A 85 PHE 0.010 0.001 PHE A 527 TYR 0.016 0.001 TYR A 555 ARG 0.001 0.000 ARG A 44 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 115 time to evaluate : 1.218 Fit side-chains REVERT: A 227 MET cc_start: 0.8026 (mmm) cc_final: 0.7698 (mmm) REVERT: A 383 MET cc_start: 0.8417 (tpp) cc_final: 0.8001 (tpt) REVERT: A 439 ASP cc_start: 0.8230 (OUTLIER) cc_final: 0.7989 (t0) REVERT: B 93 GLN cc_start: 0.6662 (OUTLIER) cc_final: 0.6378 (pt0) REVERT: B 224 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7938 (mp) outliers start: 27 outliers final: 23 residues processed: 133 average time/residue: 0.2095 time to fit residues: 41.3091 Evaluate side-chains 138 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 112 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 260 PHE Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 128 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 55 optimal weight: 0.0070 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 11226 Z= 0.334 Angle : 0.552 7.171 15233 Z= 0.279 Chirality : 0.041 0.147 1814 Planarity : 0.004 0.053 1912 Dihedral : 9.548 59.924 1717 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.38 % Allowed : 13.29 % Favored : 84.33 % 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: 0.67 (0.22), residues: 1441 helix: 1.23 (0.18), residues: 851 sheet: -0.33 (0.60), residues: 82 loop : -0.70 (0.28), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 36 HIS 0.003 0.001 HIS A 451 PHE 0.012 0.002 PHE A 373 TYR 0.021 0.002 TYR A 381 ARG 0.003 0.000 ARG B 402 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 111 time to evaluate : 1.118 Fit side-chains REVERT: A 227 MET cc_start: 0.8312 (mmm) cc_final: 0.7995 (mmm) REVERT: A 383 MET cc_start: 0.8423 (tpp) cc_final: 0.7991 (tpt) REVERT: A 439 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7984 (t0) outliers start: 27 outliers final: 22 residues processed: 127 average time/residue: 0.2119 time to fit residues: 40.2272 Evaluate side-chains 134 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 474 ASN Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 94 optimal weight: 0.0060 chunk 142 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 523 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11226 Z= 0.170 Angle : 0.487 7.060 15233 Z= 0.245 Chirality : 0.038 0.142 1814 Planarity : 0.003 0.045 1912 Dihedral : 9.237 59.758 1717 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.85 % Allowed : 13.91 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.23), residues: 1441 helix: 1.47 (0.18), residues: 851 sheet: -0.40 (0.60), residues: 84 loop : -0.63 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 71 HIS 0.002 0.000 HIS A 85 PHE 0.010 0.001 PHE A 527 TYR 0.017 0.001 TYR A 381 ARG 0.002 0.000 ARG B 363 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2882 Ramachandran restraints generated. 1441 Oldfield, 0 Emsley, 1441 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.234 Fit side-chains REVERT: A 227 MET cc_start: 0.8114 (mmm) cc_final: 0.7765 (mmm) REVERT: A 383 MET cc_start: 0.8417 (tpp) cc_final: 0.7996 (tpt) REVERT: A 439 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7963 (t0) outliers start: 21 outliers final: 20 residues processed: 123 average time/residue: 0.2109 time to fit residues: 38.8762 Evaluate side-chains 131 residues out of total 1136 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 110 time to evaluate : 1.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASP Chi-restraints excluded: chain A residue 71 MET Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 366 MET Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 439 ASP Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain B residue 19 LYS Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 188 VAL Chi-restraints excluded: chain B residue 217 ASN Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 471 THR Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 548 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 104 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 0.9980 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 197 ASN ** 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 = 0.3503 r_free = 0.3503 target = 0.133938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.106272 restraints weight = 13814.784| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.29 r_work: 0.2916 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11226 Z= 0.278 Angle : 0.526 7.136 15233 Z= 0.265 Chirality : 0.040 0.137 1814 Planarity : 0.004 0.045 1912 Dihedral : 9.273 59.417 1717 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.85 % Allowed : 14.08 % Favored : 84.07 % 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: 0.76 (0.22), residues: 1441 helix: 1.32 (0.18), residues: 852 sheet: -0.23 (0.61), residues: 80 loop : -0.71 (0.28), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 115 HIS 0.003 0.001 HIS A 451 PHE 0.010 0.001 PHE A 109 TYR 0.019 0.002 TYR A 381 ARG 0.001 0.000 ARG B 107 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2211.21 seconds wall clock time: 40 minutes 52.03 seconds (2452.03 seconds total)