Starting phenix.real_space_refine on Fri Jun 13 01:02:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z8j_39848/06_2025/8z8j_39848.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z8j_39848/06_2025/8z8j_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/cci-nas-00/data/ceres_data/8z8j_39848/06_2025/8z8j_39848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z8j_39848/06_2025/8z8j_39848.map" model { file = "/net/cci-nas-00/data/ceres_data/8z8j_39848/06_2025/8z8j_39848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z8j_39848/06_2025/8z8j_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. Time to flip 20 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.97, per 1000 atoms: 0.65 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.23 Conformation dependent library (CDL) restraints added in 2.0 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: 1.46 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: 4.21 Time building geometry restraints manager: 3.85 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: 0.00 - 2.04: 18907 2.04 - 4.08: 228 4.08 - 6.13: 27 6.13 - 8.17: 6 8.17 - 10.21: 2 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: 0.550 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 32.540 Find NCS groups from input model: 0.200 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.890 ------------------------------------------------------------------------------- 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= 0.105 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 Details of bonding type rmsd hydrogen bonds : bond 0.18599 ( 578) hydrogen bonds : angle 6.39146 ( 1612) covalent geometry : bond 0.00238 (14110) covalent geometry : angle 0.54919 (19170) *********************** 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 to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 1.880 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: 0.3360 time to fit residues: 107.7782 Evaluate side-chains 188 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 2.624 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.125681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094732 restraints weight = 49534.900| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.76 r_work: 0.2991 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 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= 0.138 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 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 578) hydrogen bonds : angle 4.95033 ( 1612) covalent geometry : bond 0.00311 (14110) covalent geometry : angle 0.56565 (19170) *********************** 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 to be fit. rotamer outliers: 8 poor density : 203 time to evaluate : 1.625 Fit side-chains REVERT: A 47 ASN cc_start: 0.8574 (t0) cc_final: 0.8116 (t0) REVERT: A 163 GLU cc_start: 0.8924 (tp30) cc_final: 0.8515 (tp30) REVERT: A 559 ASN cc_start: 0.8354 (p0) cc_final: 0.8142 (p0) REVERT: A 621 TYR cc_start: 0.8446 (m-80) cc_final: 0.8098 (m-80) REVERT: B 140 GLU cc_start: 0.8456 (tm-30) cc_final: 0.8232 (tm-30) REVERT: B 283 LYS cc_start: 0.8564 (mtpt) cc_final: 0.8332 (tppt) REVERT: B 393 MET cc_start: 0.7981 (tpt) cc_final: 0.7399 (tpt) REVERT: B 422 ASP cc_start: 0.8444 (p0) cc_final: 0.8128 (p0) REVERT: B 436 MET cc_start: 0.8951 (ttp) cc_final: 0.8724 (ttp) REVERT: B 653 GLU cc_start: 0.8525 (mp0) cc_final: 0.7943 (mp0) REVERT: C 377 ASP cc_start: 0.8646 (t0) cc_final: 0.8169 (t0) REVERT: C 378 GLN cc_start: 0.8860 (mm110) cc_final: 0.8487 (mm110) REVERT: C 410 ILE cc_start: 0.8858 (mt) cc_final: 0.8620 (mt) outliers start: 8 outliers final: 8 residues processed: 209 average time/residue: 0.3329 time to fit residues: 101.2022 Evaluate side-chains 189 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 181 time to evaluate : 1.602 ------------------------------------------------------------------------------- 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 6 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 160 optimal weight: 0.0050 chunk 76 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.126520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095654 restraints weight = 45393.363| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 3.63 r_work: 0.3012 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14110 Z= 0.108 Angle : 0.530 7.217 19170 Z= 0.267 Chirality : 0.040 0.164 2135 Planarity : 0.005 0.059 2401 Dihedral : 8.392 75.132 2033 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.07 % Allowed : 8.14 % Favored : 90.79 % 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: 1.37 (0.20), residues: 728 sheet: -0.97 (0.37), residues: 170 loop : -1.12 (0.21), residues: 755 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 41 TYR 0.031 0.001 TYR C 363 ARG 0.007 0.000 ARG B 704 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 578) hydrogen bonds : angle 4.57780 ( 1612) covalent geometry : bond 0.00238 (14110) covalent geometry : angle 0.52996 (19170) *********************** 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 221 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 205 time to evaluate : 1.644 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8502 (t0) cc_final: 0.8043 (t0) REVERT: A 48 MET cc_start: 0.7927 (ppp) cc_final: 0.7661 (ppp) REVERT: A 163 GLU cc_start: 0.8891 (tp30) cc_final: 0.8479 (tp30) REVERT: A 267 LYS cc_start: 0.8932 (mppt) cc_final: 0.8646 (tmtt) REVERT: A 365 ASP cc_start: 0.8594 (OUTLIER) cc_final: 0.8392 (m-30) REVERT: A 451 MET cc_start: 0.9178 (mtt) cc_final: 0.8819 (mtt) REVERT: A 621 TYR cc_start: 0.8426 (m-80) cc_final: 0.8126 (m-80) REVERT: B 140 GLU cc_start: 0.8495 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 393 MET cc_start: 0.8051 (tpt) cc_final: 0.7389 (tpt) REVERT: B 503 MET cc_start: 0.8932 (mpp) cc_final: 0.8655 (mpp) REVERT: B 704 ARG cc_start: 0.8975 (ttp-110) cc_final: 0.8765 (ttp-110) REVERT: C 410 ILE cc_start: 0.8896 (mt) cc_final: 0.8684 (mt) REVERT: C 423 GLN cc_start: 0.7911 (tp40) cc_final: 0.7629 (tp-100) outliers start: 16 outliers final: 11 residues processed: 215 average time/residue: 0.2702 time to fit residues: 83.3687 Evaluate side-chains 193 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 181 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 349 MET Chi-restraints excluded: chain B residue 485 THR Chi-restraints excluded: chain B residue 568 SER 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 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 53 optimal weight: 3.9990 chunk 133 optimal weight: 20.0000 chunk 25 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 122 optimal weight: 2.9990 chunk 94 optimal weight: 9.9990 chunk 107 optimal weight: 0.0570 chunk 124 optimal weight: 3.9990 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 433 HIS ** 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 = 0.3577 r_free = 0.3577 target = 0.120737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.089954 restraints weight = 36313.374| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.16 r_work: 0.2934 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2937 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2937 r_free = 0.2937 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2937 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 14110 Z= 0.202 Angle : 0.593 10.226 19170 Z= 0.299 Chirality : 0.043 0.168 2135 Planarity : 0.005 0.057 2401 Dihedral : 8.567 74.791 2033 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.47 % Allowed : 10.01 % 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: -0.07 (0.21), residues: 1653 helix: 1.29 (0.20), residues: 735 sheet: -1.18 (0.35), residues: 174 loop : -1.11 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.005 0.001 HIS C 169 PHE 0.018 0.002 PHE C 374 TYR 0.022 0.002 TYR C 382 ARG 0.008 0.001 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.03973 ( 578) hydrogen bonds : angle 4.56333 ( 1612) covalent geometry : bond 0.00480 (14110) covalent geometry : angle 0.59311 (19170) *********************** 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 209 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 187 time to evaluate : 1.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8563 (t0) cc_final: 0.7899 (t0) REVERT: A 163 GLU cc_start: 0.8887 (tp30) cc_final: 0.8462 (tp30) REVERT: A 365 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8419 (m-30) REVERT: A 437 LYS cc_start: 0.8597 (ptpt) cc_final: 0.8393 (ptpt) REVERT: A 451 MET cc_start: 0.9282 (mtt) cc_final: 0.9047 (mtt) REVERT: B 140 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8186 (tm-30) REVERT: B 283 LYS cc_start: 0.8629 (mtpt) cc_final: 0.8393 (tppt) REVERT: B 393 MET cc_start: 0.7964 (tpt) cc_final: 0.7391 (tpt) REVERT: B 422 ASP cc_start: 0.8518 (p0) cc_final: 0.8253 (p0) REVERT: B 503 MET cc_start: 0.8953 (OUTLIER) cc_final: 0.8270 (mpp) REVERT: B 682 GLU cc_start: 0.8391 (mm-30) cc_final: 0.8180 (tp30) REVERT: B 704 ARG cc_start: 0.8904 (ttp-110) cc_final: 0.8633 (ttp-110) REVERT: C 410 ILE cc_start: 0.8884 (mt) cc_final: 0.8677 (mt) REVERT: C 423 GLN cc_start: 0.8058 (tp40) cc_final: 0.7831 (tp40) outliers start: 22 outliers final: 12 residues processed: 197 average time/residue: 0.2873 time to fit residues: 81.3135 Evaluate side-chains 190 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 176 time to evaluate : 1.684 ------------------------------------------------------------------------------- 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 349 MET 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 C residue 31 MET Chi-restraints excluded: chain C residue 147 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 88 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 61 optimal weight: 0.0870 chunk 20 optimal weight: 0.0980 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 604 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.123570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.092851 restraints weight = 38374.377| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 3.33 r_work: 0.2973 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1766 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= 0.111 Angle : 0.534 9.428 19170 Z= 0.267 Chirality : 0.040 0.163 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.419 75.428 2033 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.40 % Allowed : 10.35 % Favored : 88.25 % 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: 0.05 (0.21), residues: 1653 helix: 1.39 (0.20), residues: 735 sheet: -1.07 (0.35), residues: 173 loop : -1.08 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 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 A 82 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 578) hydrogen bonds : angle 4.34991 ( 1612) covalent geometry : bond 0.00254 (14110) covalent geometry : angle 0.53364 (19170) *********************** 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 to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: A 163 GLU cc_start: 0.8884 (tp30) cc_final: 0.8433 (tp30) REVERT: A 365 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8370 (m-30) REVERT: B 140 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 422 ASP cc_start: 0.8333 (p0) cc_final: 0.8118 (p0) REVERT: B 503 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8499 (mpp) REVERT: B 682 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8149 (tp30) REVERT: B 704 ARG cc_start: 0.8907 (ttp-110) cc_final: 0.8639 (ttp-110) REVERT: C 371 LYS cc_start: 0.9071 (ttmm) cc_final: 0.8710 (ttmm) REVERT: C 410 ILE cc_start: 0.8892 (mt) cc_final: 0.8670 (mt) REVERT: C 423 GLN cc_start: 0.8025 (tp40) cc_final: 0.7772 (tp40) outliers start: 21 outliers final: 14 residues processed: 205 average time/residue: 0.3106 time to fit residues: 92.5329 Evaluate side-chains 201 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 1.513 ------------------------------------------------------------------------------- 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 349 MET Chi-restraints excluded: chain B residue 385 ILE Chi-restraints excluded: chain B residue 475 HIS 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 C residue 31 MET Chi-restraints excluded: chain C residue 147 LEU 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 89 optimal weight: 0.3980 chunk 135 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 142 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 ASN B 132 ASN B 429 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091371 restraints weight = 38009.850| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 3.28 r_work: 0.2957 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2962 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2962 r_free = 0.2962 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2962 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14110 Z= 0.139 Angle : 0.542 10.260 19170 Z= 0.272 Chirality : 0.041 0.161 2135 Planarity : 0.004 0.057 2401 Dihedral : 8.412 75.260 2033 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 1.67 % Allowed : 10.81 % Favored : 87.52 % 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: 1.44 (0.20), residues: 735 sheet: -1.08 (0.36), residues: 173 loop : -1.05 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 51 PHE 0.017 0.001 PHE C 41 TYR 0.019 0.001 TYR C 363 ARG 0.006 0.000 ARG C 198 Details of bonding type rmsd hydrogen bonds : bond 0.03401 ( 578) hydrogen bonds : angle 4.33533 ( 1612) covalent geometry : bond 0.00328 (14110) covalent geometry : angle 0.54242 (19170) *********************** 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 214 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 2.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8483 (t0) cc_final: 0.8158 (t0) REVERT: A 163 GLU cc_start: 0.8914 (tp30) cc_final: 0.8481 (tp30) REVERT: A 365 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.8399 (m-30) REVERT: A 451 MET cc_start: 0.9170 (mtt) cc_final: 0.8878 (mtt) REVERT: B 140 GLU cc_start: 0.8532 (tm-30) cc_final: 0.8233 (tm-30) REVERT: B 283 LYS cc_start: 0.8589 (mtpt) cc_final: 0.8372 (tppt) REVERT: B 393 MET cc_start: 0.7822 (tpt) cc_final: 0.7389 (tpt) REVERT: B 422 ASP cc_start: 0.8548 (p0) cc_final: 0.8328 (p0) REVERT: B 503 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8498 (mpp) REVERT: B 682 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8152 (tp30) REVERT: B 704 ARG cc_start: 0.8886 (ttp-110) cc_final: 0.8601 (ttp-110) REVERT: C 410 ILE cc_start: 0.8879 (mt) cc_final: 0.8662 (mt) REVERT: C 423 GLN cc_start: 0.8034 (tp40) cc_final: 0.7764 (tp40) outliers start: 25 outliers final: 16 residues processed: 205 average time/residue: 0.3443 time to fit residues: 105.8449 Evaluate side-chains 205 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 1.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU 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 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 349 MET Chi-restraints excluded: chain B residue 385 ILE 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 33 optimal weight: 4.9990 chunk 155 optimal weight: 20.0000 chunk 154 optimal weight: 8.9990 chunk 13 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 117 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.120829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088710 restraints weight = 57883.454| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 4.27 r_work: 0.2866 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2876 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2876 r_free = 0.2876 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2876 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.2051 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= 0.179 Angle : 0.572 10.192 19170 Z= 0.288 Chirality : 0.042 0.167 2135 Planarity : 0.004 0.056 2401 Dihedral : 8.503 75.156 2033 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.47 % Allowed : 11.35 % 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: 0.08 (0.21), residues: 1653 helix: 1.42 (0.20), residues: 735 sheet: -1.11 (0.36), residues: 173 loop : -1.03 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 336 HIS 0.006 0.001 HIS A 115 PHE 0.018 0.001 PHE C 41 TYR 0.037 0.001 TYR C 179 ARG 0.007 0.000 ARG B 687 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 578) hydrogen bonds : angle 4.39515 ( 1612) covalent geometry : bond 0.00425 (14110) covalent geometry : angle 0.57241 (19170) *********************** 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 204 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 182 time to evaluate : 1.546 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8585 (t0) cc_final: 0.8268 (t0) REVERT: A 163 GLU cc_start: 0.9001 (tp30) cc_final: 0.8590 (tp30) REVERT: A 365 ASP cc_start: 0.8717 (OUTLIER) cc_final: 0.8495 (m-30) REVERT: A 451 MET cc_start: 0.9200 (mtt) cc_final: 0.8986 (mtt) REVERT: B 140 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8345 (tm-30) REVERT: B 393 MET cc_start: 0.7856 (tpt) cc_final: 0.7614 (tpt) REVERT: B 422 ASP cc_start: 0.8737 (p0) cc_final: 0.8536 (p0) REVERT: B 499 THR cc_start: 0.8523 (OUTLIER) cc_final: 0.8077 (p) REVERT: B 503 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8405 (mpp) REVERT: B 682 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8180 (tp30) REVERT: B 704 ARG cc_start: 0.8950 (ttp-110) cc_final: 0.8654 (ttp-110) REVERT: C 371 LYS cc_start: 0.9030 (ttmm) cc_final: 0.8606 (tppt) REVERT: C 410 ILE cc_start: 0.8851 (mt) cc_final: 0.8640 (mt) REVERT: C 423 GLN cc_start: 0.8130 (tp40) cc_final: 0.7847 (tp40) outliers start: 22 outliers final: 14 residues processed: 196 average time/residue: 0.3155 time to fit residues: 91.7651 Evaluate side-chains 196 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 2.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU 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 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 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 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 66 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 156 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 64 optimal weight: 0.2980 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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 567 HIS C 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.089396 restraints weight = 51003.101| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 3.84 r_work: 0.2917 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2926 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2926 r_free = 0.2926 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2926 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14110 Z= 0.108 Angle : 0.553 11.001 19170 Z= 0.276 Chirality : 0.040 0.214 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.358 75.767 2033 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 1.27 % Allowed : 11.82 % Favored : 86.92 % 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: 0.15 (0.21), residues: 1653 helix: 1.46 (0.20), residues: 736 sheet: -1.03 (0.35), residues: 173 loop : -1.00 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.004 0.001 HIS A 115 PHE 0.019 0.001 PHE C 41 TYR 0.020 0.001 TYR C 412 ARG 0.006 0.000 ARG A 82 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 578) hydrogen bonds : angle 4.25946 ( 1612) covalent geometry : bond 0.00246 (14110) covalent geometry : angle 0.55290 (19170) *********************** 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 205 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 186 time to evaluate : 3.528 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8491 (t0) cc_final: 0.8251 (t0) REVERT: A 163 GLU cc_start: 0.8937 (tp30) cc_final: 0.8523 (tp30) REVERT: A 365 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.8413 (m-30) REVERT: A 451 MET cc_start: 0.9088 (mtt) cc_final: 0.8826 (mtt) REVERT: B 140 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8290 (tm-30) REVERT: B 283 LYS cc_start: 0.8668 (mtpt) cc_final: 0.8387 (tppt) REVERT: B 422 ASP cc_start: 0.8577 (p0) cc_final: 0.8302 (p0) REVERT: B 503 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8572 (mpp) REVERT: B 551 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8663 (pm20) REVERT: B 682 GLU cc_start: 0.8390 (mm-30) cc_final: 0.8148 (tp30) REVERT: B 704 ARG cc_start: 0.8927 (ttp-110) cc_final: 0.8626 (ttp-110) REVERT: C 371 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8650 (tppt) REVERT: C 410 ILE cc_start: 0.8909 (mt) cc_final: 0.8691 (mt) REVERT: C 423 GLN cc_start: 0.8111 (tp40) cc_final: 0.7829 (tp40) REVERT: C 472 GLU cc_start: 0.8497 (pp20) cc_final: 0.8232 (pp20) outliers start: 19 outliers final: 14 residues processed: 199 average time/residue: 0.4227 time to fit residues: 123.0440 Evaluate side-chains 193 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 203 ARG 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 392 PHE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 79 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.0980 chunk 131 optimal weight: 0.0070 chunk 75 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.121742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.090327 restraints weight = 46478.860| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 3.68 r_work: 0.2938 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2943 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2943 r_free = 0.2943 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2943 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14110 Z= 0.107 Angle : 0.555 10.345 19170 Z= 0.277 Chirality : 0.040 0.199 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.291 75.865 2033 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.40 % Allowed : 12.28 % 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: 0.22 (0.21), residues: 1653 helix: 1.53 (0.20), residues: 735 sheet: -0.95 (0.35), residues: 173 loop : -0.98 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.015 0.001 HIS A 115 PHE 0.018 0.001 PHE C 41 TYR 0.018 0.001 TYR C 363 ARG 0.006 0.000 ARG C 198 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 578) hydrogen bonds : angle 4.19900 ( 1612) covalent geometry : bond 0.00243 (14110) covalent geometry : angle 0.55515 (19170) *********************** 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 211 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 1.674 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8481 (t0) cc_final: 0.8162 (t0) REVERT: A 103 ASP cc_start: 0.8494 (t0) cc_final: 0.8168 (p0) REVERT: A 163 GLU cc_start: 0.8913 (tp30) cc_final: 0.8499 (tp30) REVERT: A 451 MET cc_start: 0.9048 (mtt) cc_final: 0.8787 (mtt) REVERT: B 140 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8278 (tm-30) REVERT: B 283 LYS cc_start: 0.8619 (mtpt) cc_final: 0.8382 (tppt) REVERT: B 422 ASP cc_start: 0.8599 (p0) cc_final: 0.8298 (p0) REVERT: B 503 MET cc_start: 0.8941 (OUTLIER) cc_final: 0.8547 (mpp) REVERT: B 551 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8660 (pm20) REVERT: B 682 GLU cc_start: 0.8382 (mm-30) cc_final: 0.8153 (tp30) REVERT: C 359 VAL cc_start: 0.8565 (p) cc_final: 0.8350 (p) REVERT: C 371 LYS cc_start: 0.8987 (ttmm) cc_final: 0.8707 (tppt) REVERT: C 410 ILE cc_start: 0.8900 (mt) cc_final: 0.8688 (mt) REVERT: C 423 GLN cc_start: 0.8085 (tp40) cc_final: 0.7800 (tp40) REVERT: C 472 GLU cc_start: 0.8412 (pp20) cc_final: 0.8153 (pp20) outliers start: 21 outliers final: 14 residues processed: 205 average time/residue: 0.2665 time to fit residues: 79.8703 Evaluate side-chains 198 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 182 time to evaluate : 1.539 ------------------------------------------------------------------------------- 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 385 ILE 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 103 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 131 optimal weight: 6.9990 chunk 141 optimal weight: 0.0030 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 78 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.122442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.091108 restraints weight = 47154.439| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.71 r_work: 0.2949 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14110 Z= 0.104 Angle : 0.554 11.619 19170 Z= 0.277 Chirality : 0.040 0.167 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.228 76.117 2033 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.07 % Allowed : 12.75 % Favored : 86.18 % 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: 0.23 (0.21), residues: 1653 helix: 1.54 (0.20), residues: 734 sheet: -0.87 (0.35), residues: 173 loop : -1.00 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 336 HIS 0.018 0.001 HIS A 115 PHE 0.018 0.001 PHE C 41 TYR 0.022 0.001 TYR C 412 ARG 0.011 0.000 ARG B 704 Details of bonding type rmsd hydrogen bonds : bond 0.03038 ( 578) hydrogen bonds : angle 4.15569 ( 1612) covalent geometry : bond 0.00237 (14110) covalent geometry : angle 0.55407 (19170) ********************** 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 207 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 191 time to evaluate : 1.533 Fit side-chains revert: symmetry clash REVERT: A 47 ASN cc_start: 0.8488 (t0) cc_final: 0.8268 (t0) REVERT: A 103 ASP cc_start: 0.8510 (t0) cc_final: 0.8274 (p0) REVERT: A 163 GLU cc_start: 0.8932 (tp30) cc_final: 0.8514 (tp30) REVERT: A 451 MET cc_start: 0.9028 (mtt) cc_final: 0.8748 (mtt) REVERT: B 140 GLU cc_start: 0.8573 (tm-30) cc_final: 0.8285 (tm-30) REVERT: B 283 LYS cc_start: 0.8635 (mtpt) cc_final: 0.8361 (tppt) REVERT: B 422 ASP cc_start: 0.8577 (p0) cc_final: 0.8268 (p0) REVERT: B 499 THR cc_start: 0.8038 (OUTLIER) cc_final: 0.7464 (m) REVERT: B 503 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8268 (mpp) REVERT: B 551 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8658 (pm20) REVERT: B 682 GLU cc_start: 0.8405 (mm-30) cc_final: 0.8155 (tp30) REVERT: C 359 VAL cc_start: 0.8513 (p) cc_final: 0.8300 (p) REVERT: C 371 LYS cc_start: 0.8980 (ttmm) cc_final: 0.8659 (tppt) REVERT: C 410 ILE cc_start: 0.8879 (mt) cc_final: 0.8666 (mt) REVERT: C 423 GLN cc_start: 0.8077 (tp40) cc_final: 0.7794 (tp40) outliers start: 16 outliers final: 12 residues processed: 201 average time/residue: 0.2778 time to fit residues: 80.8741 Evaluate side-chains 195 residues out of total 1494 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 180 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU 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 385 ILE 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 626 VAL Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain C residue 31 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 62 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 31 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 26 optimal weight: 8.9990 chunk 77 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 75 optimal weight: 0.0980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.123135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091655 restraints weight = 47885.118| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 3.75 r_work: 0.2959 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14110 Z= 0.102 Angle : 0.555 11.143 19170 Z= 0.277 Chirality : 0.040 0.199 2135 Planarity : 0.004 0.058 2401 Dihedral : 8.173 76.420 2033 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 1.13 % Allowed : 13.02 % 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: 0.30 (0.21), residues: 1653 helix: 1.60 (0.20), residues: 735 sheet: -0.80 (0.36), residues: 173 loop : -0.99 (0.22), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 336 HIS 0.012 0.001 HIS A 115 PHE 0.018 0.001 PHE C 41 TYR 0.018 0.001 TYR C 363 ARG 0.013 0.000 ARG B 704 Details of bonding type rmsd hydrogen bonds : bond 0.02959 ( 578) hydrogen bonds : angle 4.10878 ( 1612) covalent geometry : bond 0.00231 (14110) covalent geometry : angle 0.55540 (19170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7737.42 seconds wall clock time: 139 minutes 7.62 seconds (8347.62 seconds total)