Starting phenix.real_space_refine on Sun Sep 29 17:02:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn6_19388/09_2024/8rn6_19388.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn6_19388/09_2024/8rn6_19388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn6_19388/09_2024/8rn6_19388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn6_19388/09_2024/8rn6_19388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn6_19388/09_2024/8rn6_19388.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rn6_19388/09_2024/8rn6_19388.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.113 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: 5 Type Number sf(0) Gaussians S 90 5.16 5 C 7337 2.51 5 N 1955 2.21 5 O 2160 1.98 5 H 11505 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23047 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 11215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 11215 Classifications: {'peptide': 701} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 26, 'TRANS': 674} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 9935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 634, 9935 Classifications: {'peptide': 634} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 33, 'TRANS': 600} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1897 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 6, 'TRANS': 113} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 11.02, per 1000 atoms: 0.48 Number of scatterers: 23047 At special positions: 0 Unit cell: (101.64, 118.44, 120.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 O 2160 8.00 N 1955 7.00 C 7337 6.00 H 11505 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 - 3.00 Amino acid : True - 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: 5.37 Conformation dependent library (CDL) restraints added in 1.7 seconds 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 14 sheets defined 50.9% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 Processing helix chain 'A' and resid 10 through 24 removed outlier: 3.571A pdb=" N PHE A 24 " --> pdb=" O THR A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 removed outlier: 3.942A pdb=" N LEU A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 100 removed outlier: 3.595A pdb=" N MET A 90 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 139 Processing helix chain 'A' and resid 163 through 184 removed outlier: 3.838A pdb=" N ARG A 169 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU A 174 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU A 176 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 215 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 237 through 244 Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 266 through 271 Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 319 Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'A' and resid 358 through 366 removed outlier: 3.750A pdb=" N TRP A 364 " --> pdb=" O ASN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 400 through 411 removed outlier: 4.155A pdb=" N GLN A 404 " --> pdb=" O ALA A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 removed outlier: 3.609A pdb=" N GLU A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 468 removed outlier: 3.654A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 533 removed outlier: 3.511A pdb=" N ASP A 529 " --> pdb=" O PRO A 526 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER A 530 " --> pdb=" O ARG A 527 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLY A 531 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TRP A 533 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 573 Processing helix chain 'A' and resid 574 through 595 removed outlier: 4.366A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE A 594 " --> pdb=" O GLN A 590 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 629 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 3.673A pdb=" N ARG A 659 " --> pdb=" O SER A 655 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 688 Processing helix chain 'A' and resid 693 through 716 removed outlier: 3.602A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N VAL A 716 " --> pdb=" O GLU A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.013A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 118 through 122 Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 157 through 161 Processing helix chain 'B' and resid 162 through 173 removed outlier: 3.547A pdb=" N PHE B 166 " --> pdb=" O GLY B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 176 No H-bonds generated for 'chain 'B' and resid 174 through 176' Processing helix chain 'B' and resid 214 through 222 Processing helix chain 'B' and resid 245 through 264 removed outlier: 3.894A pdb=" N ARG B 249 " --> pdb=" O GLY B 245 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLY B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N PHE B 251 " --> pdb=" O GLN B 247 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 292 removed outlier: 3.736A pdb=" N LYS B 279 " --> pdb=" O GLY B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.537A pdb=" N LEU B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 338 Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 377 through 381 Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 410 through 412 No H-bonds generated for 'chain 'B' and resid 410 through 412' Processing helix chain 'B' and resid 413 through 426 Processing helix chain 'B' and resid 454 through 472 Processing helix chain 'B' and resid 517 through 536 removed outlier: 3.939A pdb=" N MET B 522 " --> pdb=" O GLU B 518 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ALA B 523 " --> pdb=" O SER B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 559 Processing helix chain 'B' and resid 571 through 582 removed outlier: 3.859A pdb=" N GLU B 577 " --> pdb=" O LYS B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.664A pdb=" N LEU B 588 " --> pdb=" O ARG B 585 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'C' and resid 44 through 54 Processing helix chain 'C' and resid 65 through 70 removed outlier: 3.631A pdb=" N ILE C 70 " --> pdb=" O ALA C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.866A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR C 99 " --> pdb=" O ILE C 95 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 117 Processing helix chain 'C' and resid 117 through 129 Processing helix chain 'C' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 79 removed outlier: 3.543A pdb=" N LEU A 110 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE A 118 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N MET A 146 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU A 120 " --> pdb=" O MET A 146 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N PHE A 148 " --> pdb=" O GLU A 120 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N GLY A 122 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.840A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.178A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS A 551 " --> pdb=" O SER A 543 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N SER A 543 " --> pdb=" O LYS A 551 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL A 553 " --> pdb=" O ILE A 541 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 323 " --> pdb=" O ARG A 540 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 291 through 295 removed outlier: 4.178A pdb=" N SER A 492 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ILE A 481 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LEU A 499 " --> pdb=" O ILE A 479 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE A 479 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL A 501 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LYS A 477 " --> pdb=" O VAL A 501 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 374 removed outlier: 6.000A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 623 through 628 removed outlier: 6.313A pdb=" N GLY A 627 " --> pdb=" O SER A 616 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N SER A 616 " --> pdb=" O GLY A 627 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA8, first strand: chain 'B' and resid 128 through 130 Processing sheet with id=AA9, first strand: chain 'B' and resid 178 through 189 removed outlier: 3.693A pdb=" N LYS B 202 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 243 through 244 Processing sheet with id=AB2, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB3, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'C' and resid 73 through 74 Processing sheet with id=AB5, first strand: chain 'C' and resid 131 through 137 removed outlier: 5.860A pdb=" N ILE C 245 " --> pdb=" O GLY C 133 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE C 135 " --> pdb=" O ARG C 243 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ARG C 243 " --> pdb=" O ILE C 135 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1608 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: 9.60 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 11477 1.03 - 1.23: 36 1.23 - 1.42: 4850 1.42 - 1.62: 6773 1.62 - 1.81: 152 Bond restraints: 23288 Sorted by residual: bond pdb=" N VAL B 255 " pdb=" CA VAL B 255 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.68e+00 bond pdb=" C PHE B 251 " pdb=" O PHE B 251 " ideal model delta sigma weight residual 1.237 1.273 -0.036 1.31e-02 5.83e+03 7.55e+00 bond pdb=" N VAL B 254 " pdb=" H VAL B 254 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 7.08e+00 bond pdb=" N LEU B 253 " pdb=" H LEU B 253 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 6.97e+00 bond pdb=" N PHE B 251 " pdb=" H PHE B 251 " ideal model delta sigma weight residual 0.860 0.913 -0.053 2.00e-02 2.50e+03 6.96e+00 ... (remaining 23283 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 39691 1.15 - 2.31: 2207 2.31 - 3.46: 169 3.46 - 4.62: 43 4.62 - 5.77: 6 Bond angle restraints: 42116 Sorted by residual: angle pdb=" CA VAL B 254 " pdb=" C VAL B 254 " pdb=" O VAL B 254 " ideal model delta sigma weight residual 120.95 116.76 4.19 1.04e+00 9.25e-01 1.63e+01 angle pdb=" N LYS B 189 " pdb=" CA LYS B 189 " pdb=" C LYS B 189 " ideal model delta sigma weight residual 108.74 113.94 -5.20 1.38e+00 5.25e-01 1.42e+01 angle pdb=" N ASN B 257 " pdb=" CA ASN B 257 " pdb=" C ASN B 257 " ideal model delta sigma weight residual 111.07 107.09 3.98 1.07e+00 8.73e-01 1.38e+01 angle pdb=" CA VAL B 252 " pdb=" C VAL B 252 " pdb=" O VAL B 252 " ideal model delta sigma weight residual 120.85 117.20 3.65 1.06e+00 8.90e-01 1.19e+01 angle pdb=" CA VAL B 255 " pdb=" C VAL B 255 " pdb=" O VAL B 255 " ideal model delta sigma weight residual 120.95 117.81 3.14 1.04e+00 9.25e-01 9.12e+00 ... (remaining 42111 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 9559 17.82 - 35.64: 929 35.64 - 53.46: 339 53.46 - 71.27: 97 71.27 - 89.09: 13 Dihedral angle restraints: 10937 sinusoidal: 6000 harmonic: 4937 Sorted by residual: dihedral pdb=" CA LEU A 507 " pdb=" C LEU A 507 " pdb=" N ARG A 508 " pdb=" CA ARG A 508 " ideal model delta harmonic sigma weight residual -180.00 -159.41 -20.59 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA ASP B 93 " pdb=" CB ASP B 93 " pdb=" CG ASP B 93 " pdb=" OD1 ASP B 93 " ideal model delta sinusoidal sigma weight residual -30.00 -88.28 58.28 1 2.00e+01 2.50e-03 1.14e+01 dihedral pdb=" CA ASP C 109 " pdb=" CB ASP C 109 " pdb=" CG ASP C 109 " pdb=" OD1 ASP C 109 " ideal model delta sinusoidal sigma weight residual -30.00 -87.96 57.96 1 2.00e+01 2.50e-03 1.13e+01 ... (remaining 10934 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1366 0.042 - 0.084: 290 0.084 - 0.127: 71 0.127 - 0.169: 7 0.169 - 0.211: 1 Chirality restraints: 1735 Sorted by residual: chirality pdb=" CA LEU B 253 " pdb=" N LEU B 253 " pdb=" C LEU B 253 " pdb=" CB LEU B 253 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 254 " pdb=" CA VAL B 254 " pdb=" CG1 VAL B 254 " pdb=" CG2 VAL B 254 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA ILE B 368 " pdb=" N ILE B 368 " pdb=" C ILE B 368 " pdb=" CB ILE B 368 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 ... (remaining 1732 not shown) Planarity restraints: 3422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 253 " 0.010 2.00e-02 2.50e+03 1.86e-02 3.45e+00 pdb=" N VAL B 254 " -0.032 2.00e-02 2.50e+03 pdb=" CA VAL B 254 " 0.008 2.00e-02 2.50e+03 pdb=" H VAL B 254 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 67 " 0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO B 68 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 68 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 68 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 254 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C VAL B 254 " 0.026 2.00e-02 2.50e+03 pdb=" O VAL B 254 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL B 255 " -0.009 2.00e-02 2.50e+03 ... (remaining 3419 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.08: 492 2.08 - 2.71: 38559 2.71 - 3.34: 68000 3.34 - 3.97: 87473 3.97 - 4.60: 138549 Nonbonded interactions: 333073 Sorted by model distance: nonbonded pdb=" OE1 GLU A 378 " pdb=" H GLU A 378 " model vdw 1.456 2.450 nonbonded pdb=" O ASP B 305 " pdb=" H SER B 477 " model vdw 1.544 2.450 nonbonded pdb=" OD1 ASN A 563 " pdb="HE21 GLN A 566 " model vdw 1.597 2.450 nonbonded pdb=" O SER A 172 " pdb=" HG1 THR A 175 " model vdw 1.597 2.450 nonbonded pdb=" O GLU B 267 " pdb=" HZ1 LYS B 281 " model vdw 1.600 2.450 ... (remaining 333068 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 10.920 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: 0.370 Extract box with map and model: 0.950 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 48.340 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11783 Z= 0.199 Angle : 0.571 5.771 15900 Z= 0.316 Chirality : 0.038 0.211 1735 Planarity : 0.004 0.053 2041 Dihedral : 17.606 89.093 4435 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 2.21 % Allowed : 26.01 % Favored : 71.78 % 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: 0.28 (0.22), residues: 1439 helix: 1.52 (0.21), residues: 648 sheet: -0.93 (0.39), residues: 161 loop : -0.90 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 437 HIS 0.002 0.000 HIS B 47 PHE 0.009 0.001 PHE B 251 TYR 0.014 0.001 TYR B 466 ARG 0.010 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 191 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 163 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 566 GLN cc_start: 0.8277 (mt0) cc_final: 0.8045 (mt0) outliers start: 28 outliers final: 24 residues processed: 188 average time/residue: 2.4193 time to fit residues: 496.9224 Evaluate side-chains 182 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 616 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 31 SER Chi-restraints excluded: chain B residue 80 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN B 276 ASN ** B 517 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.0527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11783 Z= 0.261 Angle : 0.559 5.157 15900 Z= 0.293 Chirality : 0.039 0.163 1735 Planarity : 0.004 0.046 2041 Dihedral : 6.393 58.679 1602 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 3.32 % Allowed : 23.56 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1439 helix: 1.34 (0.20), residues: 664 sheet: -0.84 (0.40), residues: 171 loop : -0.83 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 437 HIS 0.005 0.001 HIS B 47 PHE 0.011 0.001 PHE C 113 TYR 0.016 0.001 TYR B 554 ARG 0.003 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 167 time to evaluate : 1.930 Fit side-chains revert: symmetry clash REVERT: A 478 VAL cc_start: 0.9094 (OUTLIER) cc_final: 0.8853 (p) outliers start: 42 outliers final: 21 residues processed: 197 average time/residue: 2.4216 time to fit residues: 521.7087 Evaluate side-chains 183 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 161 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 358 LYS Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 59 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 73 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 0.0570 chunk 142 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 130 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11783 Z= 0.181 Angle : 0.527 5.594 15900 Z= 0.274 Chirality : 0.038 0.158 1735 Planarity : 0.004 0.049 2041 Dihedral : 5.674 58.709 1586 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 3.16 % Allowed : 23.56 % Favored : 73.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.22), residues: 1439 helix: 1.42 (0.20), residues: 667 sheet: -0.74 (0.40), residues: 169 loop : -0.94 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 PHE 0.010 0.001 PHE C 113 TYR 0.015 0.001 TYR B 554 ARG 0.004 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 1.748 Fit side-chains revert: symmetry clash REVERT: A 407 MET cc_start: 0.8737 (tpt) cc_final: 0.8494 (tpt) REVERT: A 478 VAL cc_start: 0.9092 (OUTLIER) cc_final: 0.8854 (p) REVERT: A 501 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8677 (p) REVERT: A 506 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.5851 (t-170) REVERT: B 511 PHE cc_start: 0.6142 (OUTLIER) cc_final: 0.4867 (t80) outliers start: 40 outliers final: 17 residues processed: 195 average time/residue: 2.3764 time to fit residues: 512.3513 Evaluate side-chains 181 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 160 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 130 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 62 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 140 optimal weight: 0.5980 chunk 69 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 504 GLN A 566 GLN B 276 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11783 Z= 0.264 Angle : 0.550 5.358 15900 Z= 0.286 Chirality : 0.039 0.161 1735 Planarity : 0.004 0.061 2041 Dihedral : 5.560 58.491 1582 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.73 % Favored : 95.21 % Rotamer: Outliers : 3.40 % Allowed : 23.00 % Favored : 73.60 % 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: 0.18 (0.22), residues: 1439 helix: 1.34 (0.20), residues: 666 sheet: -0.75 (0.40), residues: 171 loop : -0.99 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS B 47 PHE 0.009 0.001 PHE B 511 TYR 0.016 0.001 TYR B 554 ARG 0.006 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 207 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 164 time to evaluate : 1.695 Fit side-chains revert: symmetry clash REVERT: A 501 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 506 HIS cc_start: 0.6562 (OUTLIER) cc_final: 0.5845 (t-170) REVERT: A 528 VAL cc_start: 0.9128 (m) cc_final: 0.8807 (t) REVERT: B 353 LYS cc_start: 0.8407 (mtpt) cc_final: 0.8081 (mttm) REVERT: B 511 PHE cc_start: 0.6231 (OUTLIER) cc_final: 0.4889 (t80) REVERT: C 115 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.7167 (ttp80) REVERT: C 128 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7157 (m-30) outliers start: 43 outliers final: 25 residues processed: 196 average time/residue: 2.3585 time to fit residues: 506.8817 Evaluate side-chains 185 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 1.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 116 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 57 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 276 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11783 Z= 0.228 Angle : 0.539 5.932 15900 Z= 0.280 Chirality : 0.039 0.162 1735 Planarity : 0.004 0.063 2041 Dihedral : 5.526 58.327 1582 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 3.48 % Allowed : 22.37 % Favored : 74.15 % 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: 0.19 (0.22), residues: 1439 helix: 1.35 (0.20), residues: 666 sheet: -0.74 (0.40), residues: 171 loop : -0.97 (0.24), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.008 0.001 HIS A 41 PHE 0.010 0.001 PHE C 113 TYR 0.015 0.001 TYR B 554 ARG 0.008 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 205 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 501 VAL cc_start: 0.8922 (OUTLIER) cc_final: 0.8647 (p) REVERT: A 506 HIS cc_start: 0.6535 (OUTLIER) cc_final: 0.5832 (t-170) REVERT: A 528 VAL cc_start: 0.9109 (m) cc_final: 0.8821 (t) REVERT: B 353 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8095 (mttm) REVERT: B 511 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.4899 (t80) REVERT: C 115 ARG cc_start: 0.7494 (OUTLIER) cc_final: 0.7271 (ttp80) outliers start: 44 outliers final: 26 residues processed: 195 average time/residue: 2.4324 time to fit residues: 518.5039 Evaluate side-chains 186 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 47 optimal weight: 1.9990 chunk 126 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 276 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11783 Z= 0.268 Angle : 0.550 5.548 15900 Z= 0.286 Chirality : 0.039 0.163 1735 Planarity : 0.004 0.071 2041 Dihedral : 5.541 59.607 1582 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.66 % Favored : 95.27 % Rotamer: Outliers : 3.32 % Allowed : 22.45 % Favored : 74.23 % 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: 0.12 (0.22), residues: 1439 helix: 1.29 (0.20), residues: 670 sheet: -0.66 (0.41), residues: 164 loop : -1.06 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.004 0.001 HIS A 41 PHE 0.009 0.001 PHE B 550 TYR 0.016 0.001 TYR B 554 ARG 0.008 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 161 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8655 (p) REVERT: A 528 VAL cc_start: 0.9138 (m) cc_final: 0.8861 (t) REVERT: B 353 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8144 (mtmm) REVERT: B 511 PHE cc_start: 0.6210 (OUTLIER) cc_final: 0.5838 (m-80) REVERT: C 115 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7018 (ttp80) outliers start: 42 outliers final: 32 residues processed: 192 average time/residue: 2.4483 time to fit residues: 513.7827 Evaluate side-chains 188 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 153 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 382 ASP Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 573 LYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 136 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 135 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 87 optimal weight: 0.5980 chunk 85 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 276 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11783 Z= 0.191 Angle : 0.527 5.625 15900 Z= 0.274 Chirality : 0.038 0.162 1735 Planarity : 0.004 0.076 2041 Dihedral : 5.460 59.358 1582 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 3.79 % Allowed : 21.98 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1439 helix: 1.38 (0.20), residues: 671 sheet: -0.62 (0.41), residues: 164 loop : -0.99 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.003 0.001 HIS A 41 PHE 0.009 0.001 PHE B 550 TYR 0.014 0.001 TYR B 554 ARG 0.010 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 211 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 163 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 501 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8682 (p) REVERT: A 506 HIS cc_start: 0.6593 (OUTLIER) cc_final: 0.5877 (t-170) REVERT: A 528 VAL cc_start: 0.9075 (m) cc_final: 0.8821 (t) REVERT: B 353 LYS cc_start: 0.8414 (mtpt) cc_final: 0.8090 (mtmm) REVERT: B 511 PHE cc_start: 0.6239 (OUTLIER) cc_final: 0.5858 (m-80) REVERT: C 115 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6963 (ttp80) REVERT: C 128 ASP cc_start: 0.7505 (OUTLIER) cc_final: 0.7122 (m-30) outliers start: 48 outliers final: 31 residues processed: 200 average time/residue: 2.2945 time to fit residues: 504.4377 Evaluate side-chains 194 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 234 ASP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain B residue 618 GLU Chi-restraints excluded: chain B residue 633 HIS Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 86 ILE Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 115 ARG Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 247 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 127 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11783 Z= 0.219 Angle : 0.536 6.025 15900 Z= 0.279 Chirality : 0.039 0.162 1735 Planarity : 0.005 0.103 2041 Dihedral : 5.379 57.864 1582 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.66 % Favored : 95.27 % Rotamer: Outliers : 3.48 % Allowed : 22.37 % Favored : 74.15 % 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: 0.21 (0.22), residues: 1439 helix: 1.37 (0.20), residues: 671 sheet: -0.79 (0.41), residues: 154 loop : -0.98 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 437 HIS 0.002 0.001 HIS A 41 PHE 0.009 0.001 PHE B 550 TYR 0.017 0.001 TYR C 74 ARG 0.013 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 164 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.4275 (OUTLIER) cc_final: 0.4071 (mpp) REVERT: A 501 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8658 (p) REVERT: A 506 HIS cc_start: 0.6606 (OUTLIER) cc_final: 0.5884 (t-170) REVERT: A 528 VAL cc_start: 0.9063 (m) cc_final: 0.8826 (t) REVERT: B 353 LYS cc_start: 0.8440 (mtpt) cc_final: 0.8112 (mtmm) REVERT: B 511 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5876 (m-80) outliers start: 44 outliers final: 28 residues processed: 197 average time/residue: 2.3895 time to fit residues: 516.6497 Evaluate side-chains 190 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 158 time to evaluate : 1.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 187 TRP Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 247 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9980 chunk 130 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 129 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN B 276 ASN ** B 604 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 633 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11783 Z= 0.204 Angle : 0.532 6.348 15900 Z= 0.276 Chirality : 0.038 0.161 1735 Planarity : 0.004 0.091 2041 Dihedral : 4.699 57.432 1571 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.52 % Favored : 95.41 % Rotamer: Outliers : 3.16 % Allowed : 22.61 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1439 helix: 1.39 (0.20), residues: 672 sheet: -0.74 (0.42), residues: 154 loop : -0.95 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.002 0.001 HIS B 47 PHE 0.008 0.001 PHE B 550 TYR 0.015 0.001 TYR C 74 ARG 0.014 0.000 ARG B 622 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 163 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.4371 (OUTLIER) cc_final: 0.4167 (mpp) REVERT: A 294 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8031 (ttp) REVERT: A 501 VAL cc_start: 0.8948 (OUTLIER) cc_final: 0.8679 (p) REVERT: A 506 HIS cc_start: 0.6639 (OUTLIER) cc_final: 0.5893 (t70) REVERT: A 528 VAL cc_start: 0.9057 (m) cc_final: 0.8830 (t) REVERT: B 135 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7482 (mtm110) REVERT: B 353 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8160 (mtmm) REVERT: B 511 PHE cc_start: 0.6201 (OUTLIER) cc_final: 0.5820 (m-80) outliers start: 40 outliers final: 28 residues processed: 193 average time/residue: 2.3780 time to fit residues: 503.1958 Evaluate side-chains 196 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 163 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 513 VAL Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 712 GLU Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 573 LYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 247 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 137 optimal weight: 0.4980 chunk 84 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 95 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 132 optimal weight: 5.9990 chunk 115 optimal weight: 0.9980 chunk 11 optimal weight: 10.0000 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN B 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11783 Z= 0.190 Angle : 0.526 6.576 15900 Z= 0.272 Chirality : 0.038 0.161 1735 Planarity : 0.004 0.087 2041 Dihedral : 4.663 57.407 1571 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.45 % Favored : 95.48 % Rotamer: Outliers : 2.85 % Allowed : 23.08 % Favored : 74.07 % 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: 0.31 (0.22), residues: 1439 helix: 1.45 (0.20), residues: 671 sheet: -0.71 (0.42), residues: 154 loop : -0.93 (0.24), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.002 0.001 HIS A 41 PHE 0.008 0.001 PHE C 113 TYR 0.014 0.001 TYR B 554 ARG 0.013 0.000 ARG B 622 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2878 Ramachandran restraints generated. 1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 190 is missing expected H atoms. Skipping. Residue ILE 191 is missing expected H atoms. Skipping. Residue LYS 43 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 160 time to evaluate : 1.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.4388 (OUTLIER) cc_final: 0.4112 (mpp) REVERT: A 143 MET cc_start: 0.6548 (mtt) cc_final: 0.6256 (mtt) REVERT: A 294 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8039 (ttp) REVERT: A 350 GLU cc_start: 0.7986 (mm-30) cc_final: 0.7631 (mp0) REVERT: A 501 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8672 (p) REVERT: A 506 HIS cc_start: 0.6716 (OUTLIER) cc_final: 0.5954 (t-170) REVERT: A 528 VAL cc_start: 0.9046 (m) cc_final: 0.8826 (t) REVERT: B 135 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7512 (mtm110) REVERT: B 353 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8150 (mtmm) REVERT: B 511 PHE cc_start: 0.6203 (OUTLIER) cc_final: 0.5780 (m-80) outliers start: 36 outliers final: 25 residues processed: 188 average time/residue: 2.3996 time to fit residues: 494.6236 Evaluate side-chains 187 residues out of total 1270 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 157 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 61 TYR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 277 VAL Chi-restraints excluded: chain A residue 286 SER Chi-restraints excluded: chain A residue 294 MET Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 492 SER Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 506 HIS Chi-restraints excluded: chain A residue 523 SER Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain B residue 156 ASN Chi-restraints excluded: chain B residue 183 SER Chi-restraints excluded: chain B residue 305 ASP Chi-restraints excluded: chain B residue 372 ASP Chi-restraints excluded: chain B residue 437 TRP Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 511 PHE Chi-restraints excluded: chain B residue 517 ASN Chi-restraints excluded: chain B residue 519 SER Chi-restraints excluded: chain B residue 573 LYS Chi-restraints excluded: chain B residue 590 VAL Chi-restraints excluded: chain B residue 609 VAL Chi-restraints excluded: chain C residue 46 SER Chi-restraints excluded: chain C residue 92 MET Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 247 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 122 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 115 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN B 633 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.174859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.128397 restraints weight = 36840.981| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.83 r_work: 0.3056 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11783 Z= 0.214 Angle : 0.542 8.469 15900 Z= 0.281 Chirality : 0.038 0.163 1735 Planarity : 0.005 0.135 2041 Dihedral : 4.682 57.227 1571 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.59 % Favored : 95.34 % Rotamer: Outliers : 2.77 % Allowed : 23.40 % Favored : 73.83 % 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: 0.28 (0.22), residues: 1439 helix: 1.41 (0.20), residues: 672 sheet: -0.70 (0.42), residues: 154 loop : -0.94 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 437 HIS 0.002 0.001 HIS A 41 PHE 0.008 0.001 PHE C 113 TYR 0.015 0.001 TYR B 554 ARG 0.018 0.000 ARG B 622 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9220.77 seconds wall clock time: 160 minutes 17.57 seconds (9617.57 seconds total)