Starting phenix.real_space_refine on Fri Jun 28 10:11:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/06_2024/8z8j_39848.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/06_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_39848/06_2024/8z8j_39848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/06_2024/8z8j_39848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/06_2024/8z8j_39848.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8z8j_39848/06_2024/8z8j_39848.pdb" } 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-5370/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: 9.33, per 1000 atoms: 0.68 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: 5.43 Conformation dependent library (CDL) restraints added in 3.0 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: 1.42 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: 3.96 Time building geometry restraints manager: 5.93 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 2.440 nonbonded pdb=" OG1 THR B 295 " pdb=" O PRO B 464 " model vdw 2.256 2.440 nonbonded pdb=" ND2 ASN A 558 " pdb=" O PRO B 25 " model vdw 2.256 2.520 nonbonded pdb=" O ILE C 122 " pdb=" NE2 GLN C 207 " model vdw 2.258 2.520 nonbonded pdb=" OG1 THR B 245 " pdb=" NH2 ARG B 251 " model vdw 2.268 2.520 ... (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 ========== 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 2.310 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 40.080 Find NCS groups from input model: 0.400 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: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.200 ------------------------------------------------------------------------------- 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 : 1.607 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: 0.2586 time to fit residues: 83.3539 Evaluate side-chains 188 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 1.537 ------------------------------------------------------------------------------- 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: 0.1980 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 96 optimal weight: 0.0040 chunk 150 optimal weight: 0.9980 overall best weight: 0.8396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 500 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 ASN B 453 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14110 Z= 0.167 Angle : 0.538 7.067 19170 Z= 0.272 Chirality : 0.040 0.162 2135 Planarity : 0.005 0.060 2401 Dihedral : 8.500 75.358 2033 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.80 % Allowed : 6.61 % Favored : 92.59 % 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: 1.23 (0.20), residues: 729 sheet: -0.73 (0.37), residues: 191 loop : -1.19 (0.22), residues: 733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.005 0.001 HIS A 49 PHE 0.018 0.001 PHE C 374 TYR 0.020 0.001 TYR C 179 ARG 0.007 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 214 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 202 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7764 (m-30) cc_final: 0.7498 (m-30) REVERT: A 163 GLU cc_start: 0.8772 (tp30) cc_final: 0.8483 (tp30) REVERT: A 451 MET cc_start: 0.9106 (mtt) cc_final: 0.8609 (mtt) REVERT: B 393 MET cc_start: 0.7581 (tpt) cc_final: 0.6909 (tpt) REVERT: B 409 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7126 (mm-30) REVERT: B 436 MET cc_start: 0.8819 (ttp) cc_final: 0.8572 (ttp) REVERT: B 653 GLU cc_start: 0.8143 (mp0) cc_final: 0.7503 (mp0) REVERT: C 410 ILE cc_start: 0.8788 (mt) cc_final: 0.8555 (mt) outliers start: 12 outliers final: 11 residues processed: 211 average time/residue: 0.2649 time to fit residues: 80.4570 Evaluate side-chains 189 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 178 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 559 ASN Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 348 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 41 optimal weight: 9.9990 chunk 151 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 134 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 51 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 500 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14110 Z= 0.236 Angle : 0.547 11.112 19170 Z= 0.273 Chirality : 0.041 0.163 2135 Planarity : 0.004 0.060 2401 Dihedral : 8.509 75.313 2033 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.60 % Allowed : 7.88 % Favored : 90.52 % 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: 0.01 (0.21), residues: 1653 helix: 1.38 (0.20), residues: 728 sheet: -0.88 (0.37), residues: 181 loop : -1.15 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.004 0.001 HIS C 442 PHE 0.017 0.001 PHE C 374 TYR 0.034 0.001 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 220 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 196 time to evaluate : 1.670 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7806 (m-30) cc_final: 0.7504 (m-30) REVERT: A 163 GLU cc_start: 0.8802 (tp30) cc_final: 0.8492 (tp30) REVERT: A 451 MET cc_start: 0.9085 (mtt) cc_final: 0.8690 (mtt) REVERT: B 393 MET cc_start: 0.7568 (tpt) cc_final: 0.6974 (tpt) REVERT: B 422 ASP cc_start: 0.7992 (p0) cc_final: 0.7789 (p0) REVERT: B 704 ARG cc_start: 0.7271 (ttp-110) cc_final: 0.6827 (ttp-110) REVERT: C 145 ARG cc_start: 0.8154 (mmm-85) cc_final: 0.7942 (mmm-85) REVERT: C 410 ILE cc_start: 0.8795 (mt) cc_final: 0.8593 (mt) outliers start: 24 outliers final: 16 residues processed: 210 average time/residue: 0.2845 time to fit residues: 85.5594 Evaluate side-chains 205 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 189 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 349 MET Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 560 ASN Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain C residue 31 MET 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: 8.9990 chunk 113 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 79 optimal weight: 0.0170 chunk 143 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 500 GLN 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: 0.8606 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14110 Z= 0.285 Angle : 0.569 7.425 19170 Z= 0.288 Chirality : 0.042 0.160 2135 Planarity : 0.005 0.059 2401 Dihedral : 8.572 75.718 2033 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.27 % Allowed : 10.28 % Favored : 88.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1653 helix: 1.33 (0.20), residues: 734 sheet: -0.90 (0.36), residues: 184 loop : -1.09 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.005 0.001 HIS C 233 PHE 0.015 0.001 PHE C 41 TYR 0.025 0.001 TYR C 382 ARG 0.010 0.001 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 205 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9252 (mmmt) cc_final: 0.9037 (mmtm) REVERT: A 83 ASP cc_start: 0.7804 (m-30) cc_final: 0.7488 (m-30) REVERT: A 163 GLU cc_start: 0.8840 (tp30) cc_final: 0.8511 (tp30) REVERT: A 451 MET cc_start: 0.9075 (mtt) cc_final: 0.8772 (mtt) REVERT: B 393 MET cc_start: 0.7552 (tpt) cc_final: 0.6817 (tpt) REVERT: B 422 ASP cc_start: 0.8157 (p0) cc_final: 0.7937 (p0) REVERT: B 704 ARG cc_start: 0.7171 (ttp-110) cc_final: 0.6657 (ttp-110) REVERT: C 410 ILE cc_start: 0.8810 (mt) cc_final: 0.8608 (mt) outliers start: 19 outliers final: 12 residues processed: 196 average time/residue: 0.2659 time to fit residues: 75.2401 Evaluate side-chains 184 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 172 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 516 ASN 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 560 ASN Chi-restraints excluded: chain B residue 626 VAL Chi-restraints excluded: chain B residue 653 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 9.9990 chunk 91 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 119 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.7980 chunk 144 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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: 0.8636 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14110 Z= 0.348 Angle : 0.590 9.626 19170 Z= 0.297 Chirality : 0.043 0.160 2135 Planarity : 0.005 0.058 2401 Dihedral : 8.638 76.120 2033 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 1.80 % Allowed : 10.55 % Favored : 87.65 % 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: 1.25 (0.20), residues: 733 sheet: -0.95 (0.36), residues: 184 loop : -1.14 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.005 0.001 HIS C 233 PHE 0.019 0.002 PHE C 374 TYR 0.021 0.001 TYR C 363 ARG 0.003 0.000 ARG A 545 *********************** 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 202 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 175 time to evaluate : 1.526 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9259 (mmmt) cc_final: 0.9023 (mmtm) REVERT: A 83 ASP cc_start: 0.7786 (m-30) cc_final: 0.7453 (m-30) REVERT: A 163 GLU cc_start: 0.8869 (tp30) cc_final: 0.8536 (tp30) REVERT: B 503 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8010 (mpp) REVERT: B 682 GLU cc_start: 0.7849 (tp30) cc_final: 0.7628 (tp30) REVERT: B 704 ARG cc_start: 0.7142 (ttp-110) cc_final: 0.6612 (ttp-110) outliers start: 27 outliers final: 16 residues processed: 190 average time/residue: 0.2737 time to fit residues: 75.5968 Evaluate side-chains 187 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 170 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 560 ASN 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 348 LYS 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: 1.9990 chunk 144 optimal weight: 2.9990 chunk 31 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 160 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 84 optimal weight: 0.6980 chunk 154 optimal weight: 5.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 429 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14110 Z= 0.175 Angle : 0.532 10.857 19170 Z= 0.266 Chirality : 0.040 0.156 2135 Planarity : 0.004 0.059 2401 Dihedral : 8.533 76.432 2033 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.34 % Allowed : 11.48 % Favored : 87.18 % 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: 1.38 (0.20), residues: 733 sheet: -0.84 (0.36), residues: 184 loop : -1.10 (0.22), residues: 736 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 0.017 0.001 PHE C 41 TYR 0.020 0.001 TYR C 363 ARG 0.004 0.000 ARG C 198 *********************** 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 200 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 180 time to evaluate : 1.736 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9267 (mmmt) cc_final: 0.9036 (mmtm) REVERT: A 83 ASP cc_start: 0.7767 (m-30) cc_final: 0.7433 (m-30) REVERT: A 116 ASP cc_start: 0.8696 (p0) cc_final: 0.8341 (p0) REVERT: A 163 GLU cc_start: 0.8856 (tp30) cc_final: 0.8518 (tp30) REVERT: A 451 MET cc_start: 0.8943 (mtt) cc_final: 0.8652 (mtt) REVERT: B 393 MET cc_start: 0.7235 (tpt) cc_final: 0.6928 (tpt) REVERT: B 503 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.7973 (mpp) REVERT: B 682 GLU cc_start: 0.7785 (tp30) cc_final: 0.7524 (tp30) REVERT: B 704 ARG cc_start: 0.7088 (ttp-110) cc_final: 0.6556 (ttp-110) REVERT: C 371 LYS cc_start: 0.8806 (tppp) cc_final: 0.8228 (tppt) outliers start: 20 outliers final: 18 residues processed: 193 average time/residue: 0.2687 time to fit residues: 75.4298 Evaluate side-chains 197 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 178 time to evaluate : 1.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 377 GLU Chi-restraints excluded: chain A residue 483 PHE Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain B residue 2 ASN Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 503 MET Chi-restraints excluded: chain B residue 560 ASN 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 Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 117 optimal weight: 9.9990 chunk 90 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 159 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 429 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14110 Z= 0.320 Angle : 0.581 9.924 19170 Z= 0.292 Chirality : 0.042 0.157 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.607 76.276 2033 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.47 % Allowed : 12.08 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.21), residues: 1653 helix: 1.35 (0.20), residues: 733 sheet: -0.88 (0.36), residues: 184 loop : -1.14 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.004 0.001 HIS C 233 PHE 0.018 0.002 PHE C 374 TYR 0.034 0.002 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 197 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 175 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9263 (mmmt) cc_final: 0.9045 (mmtm) REVERT: A 83 ASP cc_start: 0.7767 (m-30) cc_final: 0.7432 (m-30) REVERT: A 163 GLU cc_start: 0.8882 (tp30) cc_final: 0.8547 (tp30) REVERT: A 451 MET cc_start: 0.8942 (mtt) cc_final: 0.8690 (mtt) REVERT: A 617 MET cc_start: 0.8534 (mtt) cc_final: 0.8327 (mtt) REVERT: B 499 THR cc_start: 0.8316 (m) cc_final: 0.7416 (m) REVERT: B 503 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.7902 (mpp) REVERT: B 682 GLU cc_start: 0.7863 (tp30) cc_final: 0.7607 (tp30) REVERT: B 704 ARG cc_start: 0.7071 (ttp-110) cc_final: 0.6541 (ttp-110) outliers start: 22 outliers final: 19 residues processed: 187 average time/residue: 0.2813 time to fit residues: 75.8139 Evaluate side-chains 188 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 138 LEU 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 483 PHE Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 538 MET 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 503 MET Chi-restraints excluded: chain B residue 560 ASN 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 Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 31 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 599 ASN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2180 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= 0.267 Angle : 0.566 11.292 19170 Z= 0.283 Chirality : 0.041 0.156 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.588 76.555 2033 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.67 % Allowed : 12.02 % 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: -0.01 (0.21), residues: 1653 helix: 1.35 (0.20), residues: 733 sheet: -0.91 (0.36), residues: 174 loop : -1.16 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.004 0.001 HIS C 233 PHE 0.017 0.001 PHE C 41 TYR 0.019 0.001 TYR C 363 ARG 0.006 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 196 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 171 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9267 (mmmt) cc_final: 0.9047 (mmtm) REVERT: A 83 ASP cc_start: 0.7767 (m-30) cc_final: 0.7429 (m-30) REVERT: A 163 GLU cc_start: 0.8895 (tp30) cc_final: 0.8558 (tp30) REVERT: A 451 MET cc_start: 0.8906 (mtt) cc_final: 0.8647 (mtt) REVERT: B 140 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7610 (tm-30) REVERT: B 210 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6705 (m-10) REVERT: B 499 THR cc_start: 0.8315 (m) cc_final: 0.7459 (m) REVERT: B 503 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7881 (mpp) REVERT: B 551 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: B 682 GLU cc_start: 0.7856 (tp30) cc_final: 0.7569 (tp30) REVERT: B 704 ARG cc_start: 0.7075 (ttp-110) cc_final: 0.6609 (ttp-110) outliers start: 25 outliers final: 20 residues processed: 183 average time/residue: 0.2604 time to fit residues: 69.9197 Evaluate side-chains 189 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 138 LEU 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 483 PHE Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 392 PHE 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 560 ASN Chi-restraints excluded: chain B residue 568 SER Chi-restraints excluded: chain B residue 599 ASN 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 Chi-restraints excluded: chain C residue 359 VAL Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 149 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 117 optimal weight: 9.9990 chunk 45 optimal weight: 8.9990 chunk 134 optimal weight: 9.9990 chunk 141 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS A 424 GLN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14110 Z= 0.333 Angle : 0.591 10.913 19170 Z= 0.297 Chirality : 0.042 0.156 2135 Planarity : 0.004 0.057 2401 Dihedral : 8.632 76.595 2033 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 1.74 % Allowed : 12.28 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1653 helix: 1.30 (0.20), residues: 734 sheet: -0.93 (0.36), residues: 174 loop : -1.20 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 336 HIS 0.008 0.001 HIS A 115 PHE 0.021 0.002 PHE C 374 TYR 0.020 0.001 TYR C 412 ARG 0.005 0.000 ARG B 687 *********************** 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 195 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 169 time to evaluate : 1.834 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9263 (mmmt) cc_final: 0.9046 (mmtm) REVERT: A 83 ASP cc_start: 0.7744 (m-30) cc_final: 0.7395 (m-30) REVERT: A 163 GLU cc_start: 0.8909 (tp30) cc_final: 0.8562 (tp30) REVERT: A 451 MET cc_start: 0.8927 (mtt) cc_final: 0.8664 (mtt) REVERT: B 140 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7600 (tm-30) REVERT: B 210 TYR cc_start: 0.7079 (OUTLIER) cc_final: 0.6740 (m-10) REVERT: B 499 THR cc_start: 0.8332 (m) cc_final: 0.7542 (m) REVERT: B 503 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.7894 (mpp) REVERT: B 551 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8583 (pm20) REVERT: B 682 GLU cc_start: 0.7895 (tp30) cc_final: 0.7423 (tp30) REVERT: B 686 ARG cc_start: 0.8249 (mmm160) cc_final: 0.8048 (tpp80) REVERT: B 704 ARG cc_start: 0.7014 (ttp-110) cc_final: 0.6660 (ttp-110) outliers start: 26 outliers final: 21 residues processed: 182 average time/residue: 0.2720 time to fit residues: 72.4290 Evaluate side-chains 187 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 138 LEU 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 483 PHE Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 MET Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 485 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 560 ASN 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 Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 165 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 131 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 101 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN B 567 HIS ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14110 Z= 0.216 Angle : 0.558 11.427 19170 Z= 0.279 Chirality : 0.041 0.198 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.565 76.768 2033 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 1.60 % Allowed : 12.42 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.21), residues: 1653 helix: 1.37 (0.20), residues: 734 sheet: -0.89 (0.36), residues: 174 loop : -1.15 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.004 0.001 HIS B 573 PHE 0.017 0.001 PHE C 41 TYR 0.018 0.001 TYR C 363 ARG 0.004 0.000 ARG B 687 ********************** 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 195 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 171 time to evaluate : 1.604 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.9272 (mmmt) cc_final: 0.9053 (mmtm) REVERT: A 83 ASP cc_start: 0.7761 (m-30) cc_final: 0.7413 (m-30) REVERT: A 163 GLU cc_start: 0.8909 (tp30) cc_final: 0.8557 (tp30) REVERT: A 451 MET cc_start: 0.8871 (mtt) cc_final: 0.8565 (mtt) REVERT: B 140 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 210 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6664 (m-10) REVERT: B 503 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7932 (mpp) REVERT: B 551 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8577 (pm20) REVERT: B 682 GLU cc_start: 0.7880 (tp30) cc_final: 0.7571 (tp30) REVERT: B 704 ARG cc_start: 0.7070 (ttp-110) cc_final: 0.6714 (ttp-110) outliers start: 24 outliers final: 21 residues processed: 184 average time/residue: 0.2646 time to fit residues: 71.6517 Evaluate side-chains 190 residues out of total 1494 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 SER Chi-restraints excluded: chain A residue 138 LEU 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 483 PHE Chi-restraints excluded: chain A residue 516 ASN Chi-restraints excluded: chain A residue 538 MET Chi-restraints excluded: chain B residue 83 SER Chi-restraints excluded: chain B residue 210 TYR Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 472 SER Chi-restraints excluded: chain B residue 485 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 560 ASN 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 Chi-restraints excluded: chain C residue 391 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 121 optimal weight: 8.9990 chunk 19 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.0170 chunk 115 optimal weight: 4.9990 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN ** C 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.120597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088500 restraints weight = 54968.758| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 4.10 r_work: 0.2882 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2894 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2894 r_free = 0.2894 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2894 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 14110 Z= 0.223 Angle : 0.555 11.346 19170 Z= 0.277 Chirality : 0.041 0.267 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.523 76.550 2033 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.67 % Allowed : 12.48 % Favored : 85.85 % 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: 0.07 (0.21), residues: 1653 helix: 1.41 (0.20), residues: 735 sheet: -0.84 (0.36), residues: 174 loop : -1.12 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 336 HIS 0.003 0.001 HIS B 573 PHE 0.020 0.001 PHE C 374 TYR 0.018 0.001 TYR C 363 ARG 0.004 0.000 ARG B 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2772.11 seconds wall clock time: 50 minutes 24.16 seconds (3024.16 seconds total)