Starting phenix.real_space_refine on Mon Aug 5 21:55:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/08_2024/8z8j_39848.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/08_2024/8z8j_39848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/08_2024/8z8j_39848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/08_2024/8z8j_39848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/08_2024/8z8j_39848.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/08_2024/8z8j_39848.cif" } resolution = 3.16 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= 0.004 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 1345 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 14 5.49 5 S 80 5.16 5 C 8698 2.51 5 N 2387 2.21 5 O 2587 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 116": "OD1" <-> "OD2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A GLU 261": "OE1" <-> "OE2" Residue "A ASP 347": "OD1" <-> "OD2" Residue "A PHE 483": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 557": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 39": "OE1" <-> "OE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 173": "OE1" <-> "OE2" Residue "B PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 297": "OE1" <-> "OE2" Residue "B ASP 301": "OD1" <-> "OD2" Residue "B ASP 423": "OD1" <-> "OD2" Residue "C ASP 37": "OD1" <-> "OD2" Residue "C TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C TYR 412": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 437": "OD1" <-> "OD2" Residue "C PHE 440": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 13766 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5021 Classifications: {'peptide': 621} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 589} Chain: "B" Number of atoms: 5255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 656, 5255 Classifications: {'peptide': 656} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 622} Chain breaks: 3 Chain: "C" Number of atoms: 3170 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 388, 3158 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 27, 'TRANS': 360} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 388, 3158 Classifications: {'peptide': 388} Link IDs: {'PTRANS': 27, 'TRANS': 360} Chain breaks: 3 bond proxies already assigned to first conformer: 3228 Chain: "D" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 237 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna2p': 3, 'rna3p': 7} Chain: "E" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 83 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ASER C 336 " occ=0.39 ... (10 atoms not shown) pdb=" OG BSER C 336 " occ=0.61 residue: pdb=" N ASER C 384 " occ=0.01 ... (10 atoms not shown) pdb=" OG BSER C 384 " occ=0.99 Time building chain proxies: 9.07, per 1000 atoms: 0.66 Number of scatterers: 13766 At special positions: 0 Unit cell: (89.8461, 101.526, 137.465, 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 80 16.00 P 14 15.00 O 2587 8.00 N 2387 7.00 C 8698 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: 5.75 Conformation dependent library (CDL) restraints added in 3.1 seconds 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3182 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 16 sheets defined 47.5% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 9 through 18 removed outlier: 4.547A pdb=" N THR A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 46 Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 126 through 133 Processing helix chain 'A' and resid 134 through 155 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 233 through 237 removed outlier: 3.548A pdb=" N ASP A 236 " --> pdb=" O LEU A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 273 through 287 removed outlier: 3.631A pdb=" N LEU A 277 " --> pdb=" O VAL A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 removed outlier: 3.734A pdb=" N ILE A 298 " --> pdb=" O HIS A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 317 removed outlier: 3.958A pdb=" N SER A 316 " --> pdb=" O SER A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 345 removed outlier: 4.165A pdb=" N GLU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG A 345 " --> pdb=" O MET A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 381 removed outlier: 4.494A pdb=" N ARG A 381 " --> pdb=" O GLU A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 401 removed outlier: 3.531A pdb=" N SER A 386 " --> pdb=" O THR A 382 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLN A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 492 Processing helix chain 'A' and resid 493 through 497 Processing helix chain 'A' and resid 498 through 516 removed outlier: 4.014A pdb=" N ASN A 516 " --> pdb=" O ARG A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 557 Processing helix chain 'A' and resid 559 through 581 removed outlier: 4.509A pdb=" N ARG A 571 " --> pdb=" O ALA A 567 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 572 " --> pdb=" O ASN A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 599 removed outlier: 3.758A pdb=" N LYS A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 615 Processing helix chain 'B' and resid 15 through 20 Processing helix chain 'B' and resid 33 through 47 removed outlier: 3.641A pdb=" N ARG B 43 " --> pdb=" O GLU B 39 " (cutoff:3.500A) Proline residue: B 44 - end of helix Processing helix chain 'B' and resid 53 through 58 Processing helix chain 'B' and resid 66 through 70 Processing helix chain 'B' and resid 80 through 94 Processing helix chain 'B' and resid 96 through 108 removed outlier: 3.792A pdb=" N LYS B 101 " --> pdb=" O PRO B 97 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LEU B 102 " --> pdb=" O ALA B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 134 through 151 Processing helix chain 'B' and resid 157 through 169 removed outlier: 3.615A pdb=" N MET B 169 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 247 through 266 removed outlier: 4.494A pdb=" N GLY B 252 " --> pdb=" O MET B 248 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N PHE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 277 Processing helix chain 'B' and resid 278 through 287 removed outlier: 3.782A pdb=" N ALA B 282 " --> pdb=" O GLU B 278 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 removed outlier: 3.538A pdb=" N GLU B 307 " --> pdb=" O LYS B 304 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS B 308 " --> pdb=" O PHE B 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 304 through 308' Processing helix chain 'B' and resid 310 through 325 removed outlier: 3.937A pdb=" N MET B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 335 Processing helix chain 'B' and resid 336 through 343 removed outlier: 3.554A pdb=" N PHE B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 406 removed outlier: 3.604A pdb=" N THR B 401 " --> pdb=" O ASN B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 432 through 449 removed outlier: 3.600A pdb=" N LYS B 448 " --> pdb=" O ARG B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 514 removed outlier: 3.598A pdb=" N ALA B 502 " --> pdb=" O MET B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 537 removed outlier: 3.547A pdb=" N TYR B 537 " --> pdb=" O TYR B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 552 removed outlier: 3.707A pdb=" N GLU B 551 " --> pdb=" O ARG B 547 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN B 552 " --> pdb=" O PHE B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 562 Processing helix chain 'B' and resid 575 through 583 Processing helix chain 'B' and resid 588 through 595 Processing helix chain 'B' and resid 646 through 666 removed outlier: 4.103A pdb=" N ASN B 650 " --> pdb=" O LYS B 646 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LYS B 651 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 671 Processing helix chain 'B' and resid 679 through 694 Processing helix chain 'B' and resid 698 through 709 Processing helix chain 'C' and resid 11 through 27 Processing helix chain 'C' and resid 27 through 32 Processing helix chain 'C' and resid 34 through 36 No H-bonds generated for 'chain 'C' and resid 34 through 36' Processing helix chain 'C' and resid 37 through 42 Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 57 through 62 removed outlier: 3.660A pdb=" N ARG C 62 " --> pdb=" O VAL C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 107 Processing helix chain 'C' and resid 115 through 123 removed outlier: 4.195A pdb=" N LEU C 123 " --> pdb=" O VAL C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 Processing helix chain 'C' and resid 166 through 176 Processing helix chain 'C' and resid 181 through 187 Processing helix chain 'C' and resid 191 through 207 Proline residue: C 202 - end of helix removed outlier: 3.620A pdb=" N LYS C 205 " --> pdb=" O GLU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 234 through 240 removed outlier: 3.575A pdb=" N GLU C 239 " --> pdb=" O PRO C 235 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N MET C 240 " --> pdb=" O ARG C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 415 removed outlier: 3.619A pdb=" N GLY C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 417 through 421 removed outlier: 3.957A pdb=" N GLY C 420 " --> pdb=" O ILE C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 446 removed outlier: 3.607A pdb=" N PHE C 435 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 455 removed outlier: 3.555A pdb=" N LEU C 451 " --> pdb=" O HIS C 447 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 59 removed outlier: 3.524A pdb=" N LYS A 97 " --> pdb=" O HIS A 115 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE A 119 " --> pdb=" O LEU A 99 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 210 through 211 removed outlier: 3.681A pdb=" N GLY B 300 " --> pdb=" O PHE B 424 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.823A pdb=" N VAL A 464 " --> pdb=" O ILE A 263 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 240 through 242 removed outlier: 6.761A pdb=" N ILE A 414 " --> pdb=" O TRP A 426 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N MET A 428 " --> pdb=" O CYS A 412 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N CYS A 412 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LEU A 430 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N THR A 410 " --> pdb=" O LEU A 430 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'A' and resid 526 through 531 Processing sheet with id=AA8, first strand: chain 'B' and resid 124 through 126 removed outlier: 3.537A pdb=" N SER B 126 " --> pdb=" O ARG B 131 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG B 131 " --> pdb=" O SER B 126 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 173 through 175 Processing sheet with id=AB1, first strand: chain 'B' and resid 242 through 245 removed outlier: 3.796A pdb=" N ASN B 227 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU B 226 " --> pdb=" O ASP B 348 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 467 through 470 Processing sheet with id=AB3, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AB4, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AB5, first strand: chain 'C' and resid 348 through 354 removed outlier: 3.510A pdb=" N LYS C 349 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU C 353 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL C 357 " --> pdb=" O LEU C 353 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 370 through 376 removed outlier: 4.319A pdb=" N GLU C 392 " --> pdb=" O ASER C 384 " (cutoff:3.500A) removed outlier: 8.331A pdb=" N THR C 482 " --> pdb=" O ASP C 391 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE C 393 " --> pdb=" O THR C 482 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 456 through 457 removed outlier: 3.520A pdb=" N LYS C 477 " --> pdb=" O ASP C 457 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1612 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: 4.27 Time building geometry restraints manager: 6.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4411 1.34 - 1.46: 2420 1.46 - 1.58: 7123 1.58 - 1.70: 27 1.70 - 1.82: 129 Bond restraints: 14110 Sorted by residual: bond pdb=" CB PRO C 343 " pdb=" CG PRO C 343 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.23e+00 bond pdb=" CB LYS C 458 " pdb=" CG LYS C 458 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.95e-01 bond pdb=" C GLU C 418 " pdb=" N PRO C 419 " ideal model delta sigma weight residual 1.334 1.355 -0.021 2.34e-02 1.83e+03 7.90e-01 bond pdb=" CA ASN A 156 " pdb=" CB ASN A 156 " ideal model delta sigma weight residual 1.530 1.545 -0.015 1.69e-02 3.50e+03 7.77e-01 bond pdb=" CB ASN C 80 " pdb=" CG ASN C 80 " ideal model delta sigma weight residual 1.516 1.538 -0.022 2.50e-02 1.60e+03 7.48e-01 ... (remaining 14105 not shown) Histogram of bond angle deviations from ideal: 99.31 - 106.27: 542 106.27 - 113.22: 7607 113.22 - 120.18: 4950 120.18 - 127.14: 5856 127.14 - 134.10: 215 Bond angle restraints: 19170 Sorted by residual: angle pdb=" N VAL C 230 " pdb=" CA VAL C 230 " pdb=" C VAL C 230 " ideal model delta sigma weight residual 112.96 107.93 5.03 1.00e+00 1.00e+00 2.53e+01 angle pdb=" C ASN A 155 " pdb=" N ASN A 156 " pdb=" CA ASN A 156 " ideal model delta sigma weight residual 121.54 127.88 -6.34 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CA PRO C 343 " pdb=" N PRO C 343 " pdb=" CD PRO C 343 " ideal model delta sigma weight residual 112.00 107.49 4.51 1.40e+00 5.10e-01 1.04e+01 angle pdb=" N GLU B 653 " pdb=" CA GLU B 653 " pdb=" CB GLU B 653 " ideal model delta sigma weight residual 110.28 115.26 -4.98 1.55e+00 4.16e-01 1.03e+01 angle pdb=" CA LEU A 402 " pdb=" CB LEU A 402 " pdb=" CG LEU A 402 " ideal model delta sigma weight residual 116.30 126.51 -10.21 3.50e+00 8.16e-02 8.51e+00 ... (remaining 19165 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 7820 17.95 - 35.90: 641 35.90 - 53.85: 103 53.85 - 71.80: 30 71.80 - 89.75: 11 Dihedral angle restraints: 8605 sinusoidal: 3706 harmonic: 4899 Sorted by residual: dihedral pdb=" CA GLU C 418 " pdb=" C GLU C 418 " pdb=" N PRO C 419 " pdb=" CA PRO C 419 " ideal model delta harmonic sigma weight residual 180.00 -162.13 -17.87 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CB GLU B 372 " pdb=" CG GLU B 372 " pdb=" CD GLU B 372 " pdb=" OE1 GLU B 372 " ideal model delta sinusoidal sigma weight residual 0.00 89.75 -89.75 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CB GLU B 550 " pdb=" CG GLU B 550 " pdb=" CD GLU B 550 " pdb=" OE1 GLU B 550 " ideal model delta sinusoidal sigma weight residual 0.00 -88.89 88.89 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1387 0.032 - 0.064: 511 0.064 - 0.095: 165 0.095 - 0.127: 64 0.127 - 0.159: 8 Chirality restraints: 2135 Sorted by residual: chirality pdb=" CB ILE B 620 " pdb=" CA ILE B 620 " pdb=" CG1 ILE B 620 " pdb=" CG2 ILE B 620 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.31e-01 chirality pdb=" CA ASN A 156 " pdb=" N ASN A 156 " pdb=" C ASN A 156 " pdb=" CB ASN A 156 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CA GLU C 405 " pdb=" N GLU C 405 " pdb=" C GLU C 405 " pdb=" CB GLU C 405 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.23e-01 ... (remaining 2132 not shown) Planarity restraints: 2401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 342 " 0.046 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO C 343 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 343 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 343 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 234 " -0.040 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO C 235 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 96 " -0.037 5.00e-02 4.00e+02 5.64e-02 5.09e+00 pdb=" N PRO B 97 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 97 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 97 " -0.032 5.00e-02 4.00e+02 ... (remaining 2398 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1765 2.75 - 3.29: 13745 3.29 - 3.83: 23114 3.83 - 4.36: 27698 4.36 - 4.90: 47543 Nonbonded interactions: 113865 Sorted by model distance: nonbonded pdb=" O SER A 482 " pdb=" O2' A D 3 " model vdw 2.218 3.040 nonbonded pdb=" OG1 THR B 295 " pdb=" O PRO B 464 " model vdw 2.256 3.040 nonbonded pdb=" ND2 ASN A 558 " pdb=" O PRO B 25 " model vdw 2.256 3.120 nonbonded pdb=" O ILE C 122 " pdb=" NE2 GLN C 207 " model vdw 2.258 3.120 nonbonded pdb=" OG1 THR B 245 " pdb=" NH2 ARG B 251 " model vdw 2.268 3.120 ... (remaining 113860 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=0.01 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 40.480 Find NCS groups from input model: 0.180 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 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 : 0.002 0.075 14110 Z= 0.164 Angle : 0.549 10.211 19170 Z= 0.279 Chirality : 0.040 0.159 2135 Planarity : 0.005 0.067 2401 Dihedral : 13.582 89.746 5423 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 (0.21), residues: 1653 helix: 1.02 (0.20), residues: 721 sheet: -0.55 (0.40), residues: 172 loop : -1.25 (0.21), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 220 HIS 0.007 0.001 HIS C 442 PHE 0.029 0.001 PHE B 290 TYR 0.023 0.001 TYR B 176 ARG 0.011 0.000 ARG B 704 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 1.780 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8160 (t0) cc_final: 0.6862 (t0) REVERT: A 83 ASP cc_start: 0.7768 (m-30) cc_final: 0.7518 (m-30) REVERT: A 163 GLU cc_start: 0.8831 (tp30) cc_final: 0.8510 (tp30) REVERT: A 447 ILE cc_start: 0.9270 (mm) cc_final: 0.9052 (mm) REVERT: B 393 MET cc_start: 0.7460 (tpt) cc_final: 0.6911 (tpt) REVERT: B 422 ASP cc_start: 0.7992 (p0) cc_final: 0.7783 (p0) REVERT: B 653 GLU cc_start: 0.8184 (mp0) cc_final: 0.7647 (mp0) REVERT: C 378 GLN cc_start: 0.8881 (mm110) cc_final: 0.8522 (mm110) REVERT: C 405 GLU cc_start: 0.7240 (pp20) cc_final: 0.6954 (pp20) REVERT: C 410 ILE cc_start: 0.8818 (mt) cc_final: 0.8552 (mt) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.2675 time to fit residues: 85.5376 Evaluate side-chains 188 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 0.0070 chunk 96 optimal weight: 0.0970 chunk 150 optimal weight: 9.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 129 HIS B 336 ASN B 453 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 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 : 0.003 0.040 14110 Z= 0.208 Angle : 0.566 7.109 19170 Z= 0.289 Chirality : 0.041 0.163 2135 Planarity : 0.005 0.059 2401 Dihedral : 8.481 74.670 2033 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.53 % Allowed : 6.81 % Favored : 92.66 % 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 (0.21), residues: 1653 helix: 1.21 (0.20), residues: 728 sheet: -0.80 (0.38), residues: 180 loop : -1.20 (0.21), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.006 0.001 HIS A 49 PHE 0.018 0.001 PHE C 374 TYR 0.023 0.001 TYR C 382 ARG 0.006 0.000 ARG B 704 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 203 time to evaluate : 1.892 Fit side-chains REVERT: A 47 ASN cc_start: 0.7860 (t0) cc_final: 0.7407 (t0) REVERT: A 83 ASP cc_start: 0.7864 (m-30) cc_final: 0.7612 (m-30) REVERT: A 163 GLU cc_start: 0.8821 (tp30) cc_final: 0.8541 (tp30) REVERT: A 621 TYR cc_start: 0.8427 (m-80) cc_final: 0.8153 (m-80) REVERT: B 393 MET cc_start: 0.7516 (tpt) cc_final: 0.6865 (tpt) REVERT: B 422 ASP cc_start: 0.7985 (p0) cc_final: 0.7661 (p0) REVERT: B 436 MET cc_start: 0.8838 (ttp) cc_final: 0.8623 (ttp) REVERT: B 503 MET cc_start: 0.8506 (mpp) cc_final: 0.8279 (mpp) REVERT: B 653 GLU cc_start: 0.8213 (mp0) cc_final: 0.7593 (mp0) REVERT: C 377 ASP cc_start: 0.8621 (t0) cc_final: 0.8120 (t0) REVERT: C 378 GLN cc_start: 0.8877 (mm110) cc_final: 0.8496 (mm110) REVERT: C 410 ILE cc_start: 0.8771 (mt) cc_final: 0.8543 (mt) outliers start: 8 outliers final: 8 residues processed: 209 average time/residue: 0.2771 time to fit residues: 83.6795 Evaluate side-chains 189 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 181 time to evaluate : 1.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 151 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 134 optimal weight: 4.9990 chunk 149 optimal weight: 8.9990 chunk 51 optimal weight: 0.9990 chunk 121 optimal weight: 8.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14110 Z= 0.249 Angle : 0.561 7.236 19170 Z= 0.284 Chirality : 0.041 0.160 2135 Planarity : 0.005 0.058 2401 Dihedral : 8.511 74.854 2033 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.13 % Allowed : 8.54 % Favored : 90.32 % 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: -0.05 (0.21), residues: 1653 helix: 1.31 (0.20), residues: 729 sheet: -1.04 (0.37), residues: 170 loop : -1.14 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS C 442 PHE 0.018 0.001 PHE C 374 TYR 0.033 0.002 TYR C 363 ARG 0.006 0.000 ARG B 704 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 197 time to evaluate : 1.577 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7923 (m-30) cc_final: 0.7621 (m-30) REVERT: A 163 GLU cc_start: 0.8848 (tp30) cc_final: 0.8562 (tp30) REVERT: A 267 LYS cc_start: 0.8905 (mppt) cc_final: 0.8667 (tmtt) REVERT: A 365 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.8260 (m-30) REVERT: A 451 MET cc_start: 0.9068 (mtt) cc_final: 0.8697 (mtt) REVERT: B 393 MET cc_start: 0.7550 (tpt) cc_final: 0.6869 (tpt) REVERT: B 422 ASP cc_start: 0.8055 (p0) cc_final: 0.7748 (p0) REVERT: B 503 MET cc_start: 0.8450 (OUTLIER) cc_final: 0.8005 (mpp) REVERT: B 704 ARG cc_start: 0.7191 (ttp-110) cc_final: 0.6750 (ttp-110) REVERT: C 145 ARG cc_start: 0.8172 (mmm-85) cc_final: 0.7956 (mmm-85) REVERT: C 410 ILE cc_start: 0.8814 (mt) cc_final: 0.8613 (mt) outliers start: 17 outliers final: 10 residues processed: 207 average time/residue: 0.2922 time to fit residues: 86.0484 Evaluate side-chains 198 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 186 time to evaluate : 1.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 629 CYS Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 348 LYS Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 78 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 151 optimal weight: 10.0000 chunk 160 optimal weight: 0.6980 chunk 79 optimal weight: 5.9990 chunk 143 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 ASN B 429 ASN B 433 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14110 Z= 0.294 Angle : 0.572 7.271 19170 Z= 0.289 Chirality : 0.042 0.174 2135 Planarity : 0.005 0.057 2401 Dihedral : 8.566 74.900 2033 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.27 % Allowed : 10.21 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.21), residues: 1653 helix: 1.26 (0.20), residues: 735 sheet: -1.14 (0.36), residues: 174 loop : -1.12 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 PHE 0.018 0.002 PHE C 374 TYR 0.022 0.001 TYR C 382 ARG 0.005 0.000 ARG C 198 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7939 (t0) cc_final: 0.7630 (t0) REVERT: A 76 LYS cc_start: 0.9273 (mmmt) cc_final: 0.9053 (mmtm) REVERT: A 83 ASP cc_start: 0.7929 (m-30) cc_final: 0.7582 (m-30) REVERT: A 163 GLU cc_start: 0.8881 (tp30) cc_final: 0.8575 (tp30) REVERT: A 365 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: A 451 MET cc_start: 0.9071 (mtt) cc_final: 0.8764 (mtt) REVERT: B 422 ASP cc_start: 0.8199 (p0) cc_final: 0.7915 (p0) REVERT: B 503 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7995 (mpp) REVERT: B 704 ARG cc_start: 0.7162 (ttp-110) cc_final: 0.6652 (ttp-110) outliers start: 19 outliers final: 10 residues processed: 195 average time/residue: 0.2833 time to fit residues: 79.2855 Evaluate side-chains 190 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 chunk 119 optimal weight: 9.9990 chunk 66 optimal weight: 0.2980 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN A 424 GLN B 429 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14110 Z= 0.253 Angle : 0.559 10.744 19170 Z= 0.281 Chirality : 0.041 0.161 2135 Planarity : 0.004 0.057 2401 Dihedral : 8.538 75.106 2033 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.67 % Allowed : 10.35 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.21), residues: 1653 helix: 1.29 (0.20), residues: 735 sheet: -1.13 (0.36), residues: 173 loop : -1.11 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 PHE 0.018 0.001 PHE C 41 TYR 0.021 0.001 TYR C 363 ARG 0.003 0.000 ARG B 704 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 187 time to evaluate : 1.540 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7937 (t0) cc_final: 0.7593 (t0) REVERT: A 76 LYS cc_start: 0.9261 (mmmt) cc_final: 0.8993 (mmtm) REVERT: A 83 ASP cc_start: 0.7895 (m-30) cc_final: 0.7515 (m-30) REVERT: A 163 GLU cc_start: 0.8899 (tp30) cc_final: 0.8588 (tp30) REVERT: A 365 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.8285 (m-30) REVERT: B 393 MET cc_start: 0.7344 (tpt) cc_final: 0.7030 (tpt) REVERT: B 499 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7677 (p) REVERT: B 503 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.8017 (mpp) REVERT: B 704 ARG cc_start: 0.7124 (ttp-110) cc_final: 0.6593 (ttp-110) REVERT: C 423 GLN cc_start: 0.7930 (tp40) cc_final: 0.7650 (tp-100) outliers start: 25 outliers final: 18 residues processed: 203 average time/residue: 0.2821 time to fit residues: 82.8942 Evaluate side-chains 199 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 6.9990 chunk 144 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 94 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 160 optimal weight: 0.0670 chunk 133 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 13 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 154 optimal weight: 5.9990 overall best weight: 1.0240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 567 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14110 Z= 0.172 Angle : 0.529 9.917 19170 Z= 0.266 Chirality : 0.040 0.162 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.396 75.536 2033 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.54 % Allowed : 11.08 % Favored : 87.38 % 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: 0.08 (0.21), residues: 1653 helix: 1.43 (0.20), residues: 735 sheet: -1.06 (0.35), residues: 173 loop : -1.07 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 PHE 0.019 0.001 PHE C 41 TYR 0.019 0.001 TYR C 363 ARG 0.007 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 1.572 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9281 (mmmt) cc_final: 0.9050 (mmtm) REVERT: A 83 ASP cc_start: 0.7880 (m-30) cc_final: 0.7510 (m-30) REVERT: A 163 GLU cc_start: 0.8879 (tp30) cc_final: 0.8558 (tp30) REVERT: A 365 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8241 (m-30) REVERT: A 451 MET cc_start: 0.8913 (mtt) cc_final: 0.8615 (mtt) REVERT: B 140 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 393 MET cc_start: 0.7275 (tpt) cc_final: 0.7008 (tpt) REVERT: B 499 THR cc_start: 0.8056 (OUTLIER) cc_final: 0.6972 (m) REVERT: B 503 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7710 (mpp) REVERT: B 704 ARG cc_start: 0.7087 (ttp-110) cc_final: 0.6575 (ttp-110) REVERT: C 371 LYS cc_start: 0.9061 (ttmm) cc_final: 0.8848 (ttmm) outliers start: 23 outliers final: 14 residues processed: 201 average time/residue: 0.2702 time to fit residues: 78.1541 Evaluate side-chains 194 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 177 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 359 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.5980 chunk 91 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 89 optimal weight: 0.1980 chunk 159 optimal weight: 0.8980 chunk 100 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14110 Z= 0.155 Angle : 0.530 8.146 19170 Z= 0.265 Chirality : 0.040 0.170 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.305 75.783 2033 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.34 % Allowed : 11.82 % Favored : 86.85 % 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 (0.21), residues: 1653 helix: 1.51 (0.20), residues: 735 sheet: -0.98 (0.36), residues: 173 loop : -1.01 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.006 0.001 HIS B 475 PHE 0.018 0.001 PHE C 41 TYR 0.036 0.001 TYR C 179 ARG 0.008 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 186 time to evaluate : 1.504 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.7891 (t0) cc_final: 0.7633 (t0) REVERT: A 76 LYS cc_start: 0.9278 (mmmt) cc_final: 0.9051 (mmtm) REVERT: A 83 ASP cc_start: 0.7898 (m-30) cc_final: 0.7528 (m-30) REVERT: A 163 GLU cc_start: 0.8885 (tp30) cc_final: 0.8567 (tp30) REVERT: A 451 MET cc_start: 0.8894 (mtt) cc_final: 0.8579 (mtt) REVERT: A 617 MET cc_start: 0.8496 (mtt) cc_final: 0.8228 (mtt) REVERT: B 140 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7615 (tm-30) REVERT: B 499 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.6936 (m) REVERT: B 503 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7705 (mpp) REVERT: B 551 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8626 (pm20) REVERT: B 697 LEU cc_start: 0.8857 (mm) cc_final: 0.8626 (mt) REVERT: B 704 ARG cc_start: 0.7058 (ttp-110) cc_final: 0.6542 (ttp-110) REVERT: C 371 LYS cc_start: 0.9009 (ttmm) cc_final: 0.8752 (ttmm) REVERT: C 423 GLN cc_start: 0.7832 (tp40) cc_final: 0.7608 (tp-100) REVERT: C 472 GLU cc_start: 0.8482 (pp20) cc_final: 0.8205 (pp20) outliers start: 20 outliers final: 15 residues processed: 200 average time/residue: 0.2732 time to fit residues: 78.8814 Evaluate side-chains 195 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 177 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.0470 chunk 95 optimal weight: 0.0470 chunk 48 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 0.2980 chunk 14 optimal weight: 7.9990 chunk 125 optimal weight: 0.7980 chunk 145 optimal weight: 0.8980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14110 Z= 0.146 Angle : 0.528 10.077 19170 Z= 0.265 Chirality : 0.040 0.221 2135 Planarity : 0.004 0.059 2401 Dihedral : 8.220 76.160 2033 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.20 % Allowed : 12.22 % Favored : 86.58 % 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 (0.21), residues: 1653 helix: 1.56 (0.20), residues: 735 sheet: -0.87 (0.35), residues: 174 loop : -0.98 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS B 475 PHE 0.018 0.001 PHE C 41 TYR 0.018 0.001 TYR C 363 ARG 0.005 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 1.630 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9316 (mmmt) cc_final: 0.9069 (mmtm) REVERT: A 83 ASP cc_start: 0.7948 (m-30) cc_final: 0.7564 (m-30) REVERT: A 103 ASP cc_start: 0.7576 (t0) cc_final: 0.7231 (p0) REVERT: A 106 ASP cc_start: 0.8444 (p0) cc_final: 0.8011 (p0) REVERT: A 163 GLU cc_start: 0.8880 (tp30) cc_final: 0.8599 (tp30) REVERT: A 451 MET cc_start: 0.8827 (mtt) cc_final: 0.8502 (mtt) REVERT: A 617 MET cc_start: 0.8426 (mtt) cc_final: 0.8182 (mtt) REVERT: B 140 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7629 (tm-30) REVERT: B 503 MET cc_start: 0.8410 (OUTLIER) cc_final: 0.8017 (mpp) REVERT: B 551 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8609 (pm20) REVERT: B 697 LEU cc_start: 0.8848 (mm) cc_final: 0.8645 (mt) REVERT: B 704 ARG cc_start: 0.7044 (ttp-110) cc_final: 0.6581 (ttp-110) REVERT: C 371 LYS cc_start: 0.8994 (ttmm) cc_final: 0.8752 (ttmm) REVERT: C 423 GLN cc_start: 0.7797 (tp40) cc_final: 0.7561 (tp-100) REVERT: C 472 GLU cc_start: 0.8472 (pp20) cc_final: 0.8206 (pp20) outliers start: 18 outliers final: 12 residues processed: 200 average time/residue: 0.2602 time to fit residues: 76.2445 Evaluate side-chains 195 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 181 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 6.9990 chunk 139 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 141 optimal weight: 0.0970 chunk 148 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14110 Z= 0.154 Angle : 0.523 7.322 19170 Z= 0.263 Chirality : 0.040 0.177 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.187 76.258 2033 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.27 % Allowed : 12.42 % Favored : 86.32 % 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: 0.29 (0.21), residues: 1653 helix: 1.56 (0.20), residues: 740 sheet: -0.80 (0.36), residues: 173 loop : -0.97 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.006 0.001 HIS A 115 PHE 0.018 0.001 PHE C 41 TYR 0.021 0.001 TYR C 412 ARG 0.004 0.000 ARG A 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.639 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9357 (mmmt) cc_final: 0.9121 (mmtm) REVERT: A 83 ASP cc_start: 0.7951 (m-30) cc_final: 0.7602 (m-30) REVERT: A 103 ASP cc_start: 0.7608 (t0) cc_final: 0.7183 (p0) REVERT: A 163 GLU cc_start: 0.8872 (tp30) cc_final: 0.8607 (tp30) REVERT: A 451 MET cc_start: 0.8797 (mtt) cc_final: 0.8479 (mtt) REVERT: A 617 MET cc_start: 0.8479 (mtt) cc_final: 0.8251 (mtt) REVERT: B 140 GLU cc_start: 0.7881 (tm-30) cc_final: 0.7613 (tm-30) REVERT: B 210 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.6811 (m-10) REVERT: B 499 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7661 (p) REVERT: B 503 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.8024 (mpp) REVERT: B 551 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8604 (pm20) REVERT: B 697 LEU cc_start: 0.8849 (mm) cc_final: 0.8638 (mt) REVERT: B 704 ARG cc_start: 0.7040 (ttp-110) cc_final: 0.6693 (ttp-110) REVERT: C 423 GLN cc_start: 0.7822 (tp40) cc_final: 0.7577 (tp-100) REVERT: C 472 GLU cc_start: 0.8444 (pp20) cc_final: 0.8172 (pp20) outliers start: 19 outliers final: 11 residues processed: 198 average time/residue: 0.2654 time to fit residues: 77.2606 Evaluate side-chains 196 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 181 time to evaluate : 1.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 20.0000 chunk 96 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 109 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 152 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 104 optimal weight: 0.7980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN B 475 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14110 Z= 0.200 Angle : 0.543 10.852 19170 Z= 0.272 Chirality : 0.041 0.168 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.250 76.050 2033 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.20 % Allowed : 12.55 % Favored : 86.25 % 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: 0.30 (0.21), residues: 1653 helix: 1.59 (0.20), residues: 735 sheet: -0.79 (0.36), residues: 172 loop : -0.97 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 PHE 0.017 0.001 PHE C 41 TYR 0.018 0.001 TYR C 363 ARG 0.003 0.000 ARG B 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3306 Ramachandran restraints generated. 1653 Oldfield, 0 Emsley, 1653 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 181 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: A 65 ARG cc_start: 0.8218 (tpp-160) cc_final: 0.8006 (tpp-160) REVERT: A 76 LYS cc_start: 0.9344 (mmmt) cc_final: 0.9117 (mmtm) REVERT: A 83 ASP cc_start: 0.7916 (m-30) cc_final: 0.7560 (m-30) REVERT: A 163 GLU cc_start: 0.8886 (tp30) cc_final: 0.8641 (tp30) REVERT: A 451 MET cc_start: 0.8831 (mtt) cc_final: 0.8528 (mtt) REVERT: B 140 GLU cc_start: 0.7890 (tm-30) cc_final: 0.7606 (tm-30) REVERT: B 210 TYR cc_start: 0.7092 (OUTLIER) cc_final: 0.6832 (m-10) REVERT: B 499 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.6986 (m) REVERT: B 503 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.7689 (mpp) REVERT: B 551 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8601 (pm20) REVERT: B 704 ARG cc_start: 0.7031 (ttp-110) cc_final: 0.6553 (ttp-110) REVERT: C 423 GLN cc_start: 0.7864 (tp40) cc_final: 0.7606 (tp-100) REVERT: C 472 GLU cc_start: 0.8427 (pp20) cc_final: 0.8154 (pp20) outliers start: 18 outliers final: 12 residues processed: 193 average time/residue: 0.2561 time to fit residues: 72.2048 Evaluate side-chains 191 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 175 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 430 LEU Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 499 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 531 HIS Chi-restraints excluded: chain B residue 551 GLU Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Chi-restraints excluded: chain C residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 0.0000 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.123326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.091607 restraints weight = 54194.481| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 3.90 r_work: 0.2936 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2945 r_free = 0.2945 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.2945 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14110 Z= 0.155 Angle : 0.539 11.363 19170 Z= 0.270 Chirality : 0.040 0.196 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.184 76.449 2033 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.27 % Allowed : 12.62 % Favored : 86.11 % 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 (0.21), residues: 1653 helix: 1.58 (0.20), residues: 741 sheet: -0.71 (0.36), residues: 172 loop : -0.98 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 PHE 0.019 0.001 PHE C 41 TYR 0.020 0.001 TYR C 412 ARG 0.004 0.000 ARG A 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2918.57 seconds wall clock time: 53 minutes 11.82 seconds (3191.82 seconds total)