Starting phenix.real_space_refine on Wed Feb 14 23:50:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2024/6t0w_10361.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2024/6t0w_10361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2024/6t0w_10361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2024/6t0w_10361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2024/6t0w_10361.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t0w_10361/02_2024/6t0w_10361.pdb" } resolution = 3.18 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 25 5.49 5 S 79 5.16 5 C 6599 2.51 5 N 1806 2.21 5 O 2047 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10556 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 521, 4161 Classifications: {'peptide': 521} Link IDs: {'PTRANS': 21, 'TRANS': 499} Chain: "B" Number of atoms: 5174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 661, 5174 Classifications: {'peptide': 661} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 627} Chain breaks: 1 Chain: "C" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 688 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "V" Number of atoms: 533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 533 Classifications: {'RNA': 25} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 10, 'rna3p_pyr': 9} Link IDs: {'rna2p': 6, 'rna3p': 18} Chain breaks: 2 Time building chain proxies: 6.06, per 1000 atoms: 0.57 Number of scatterers: 10556 At special positions: 0 Unit cell: (104.009, 101.908, 113.465, 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 79 16.00 P 25 15.00 O 2047 8.00 N 1806 7.00 C 6599 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.95 Conformation dependent library (CDL) restraints added in 1.8 seconds 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2352 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 11 sheets defined 47.4% alpha, 12.0% beta 6 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 206 through 214 Processing helix chain 'A' and resid 222 through 233 removed outlier: 3.804A pdb=" N MET A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 245 removed outlier: 4.213A pdb=" N ARG A 241 " --> pdb=" O GLY A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 270 removed outlier: 3.564A pdb=" N ILE A 269 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N TYR A 270 " --> pdb=" O PRO A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 270' Processing helix chain 'A' and resid 301 through 313 Processing helix chain 'A' and resid 313 through 318 removed outlier: 3.684A pdb=" N ARG A 317 " --> pdb=" O TYR A 313 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP A 318 " --> pdb=" O SER A 314 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 313 through 318' Processing helix chain 'A' and resid 332 through 347 Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 376 through 383 Processing helix chain 'A' and resid 401 through 410 removed outlier: 3.631A pdb=" N THR A 405 " --> pdb=" O ALA A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 447 removed outlier: 3.845A pdb=" N ASN A 444 " --> pdb=" O LYS A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 472 removed outlier: 3.942A pdb=" N THR A 453 " --> pdb=" O CYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.566A pdb=" N TRP A 533 " --> pdb=" O SER A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 574 through 592 removed outlier: 3.921A pdb=" N LEU A 578 " --> pdb=" O ARG A 574 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N GLN A 590 " --> pdb=" O ALA A 586 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLU A 591 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 605 Processing helix chain 'A' and resid 628 through 646 Processing helix chain 'A' and resid 648 through 670 removed outlier: 4.594A pdb=" N ARG A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LEU A 661 " --> pdb=" O GLU A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 687 removed outlier: 3.598A pdb=" N MET A 682 " --> pdb=" O ASP A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 715 removed outlier: 3.687A pdb=" N LYS A 715 " --> pdb=" O LYS A 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 12 removed outlier: 4.185A pdb=" N ASP B 11 " --> pdb=" O PHE B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 3.608A pdb=" N THR B 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 Processing helix chain 'B' and resid 84 through 99 Processing helix chain 'B' and resid 101 through 115 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 138 through 151 Processing helix chain 'B' and resid 152 through 154 No H-bonds generated for 'chain 'B' and resid 152 through 154' Processing helix chain 'B' and resid 163 through 174 removed outlier: 3.805A pdb=" N LEU B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 222 Processing helix chain 'B' and resid 248 through 265 removed outlier: 3.840A pdb=" N VAL B 254 " --> pdb=" O GLY B 250 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN B 265 " --> pdb=" O ASN B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 291 Processing helix chain 'B' and resid 308 through 313 removed outlier: 3.610A pdb=" N LEU B 313 " --> pdb=" O TRP B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 Processing helix chain 'B' and resid 330 through 337 Processing helix chain 'B' and resid 339 through 345 Processing helix chain 'B' and resid 370 through 375 removed outlier: 3.528A pdb=" N LEU B 373 " --> pdb=" O CYS B 370 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N PHE B 374 " --> pdb=" O PRO B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 381 removed outlier: 3.507A pdb=" N TYR B 381 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 393 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 415 through 426 Processing helix chain 'B' and resid 454 through 471 removed outlier: 3.746A pdb=" N LEU B 471 " --> pdb=" O ARG B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 517 through 536 Processing helix chain 'B' and resid 539 through 558 Processing helix chain 'B' and resid 571 through 582 Processing helix chain 'B' and resid 584 through 588 removed outlier: 3.924A pdb=" N GLY B 587 " --> pdb=" O GLY B 584 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 588 " --> pdb=" O ARG B 585 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 584 through 588' Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 606 through 612 Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 616 through 624 Processing helix chain 'C' and resid 45 through 55 Processing helix chain 'C' and resid 65 through 70 Processing helix chain 'C' and resid 94 through 105 removed outlier: 3.655A pdb=" N VAL C 98 " --> pdb=" O SER C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 128 removed outlier: 3.602A pdb=" N PHE C 121 " --> pdb=" O TYR C 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 255 through 256 removed outlier: 3.550A pdb=" N GLY B 304 " --> pdb=" O PHE B 446 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE B 446 " --> pdb=" O GLY B 304 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 294 removed outlier: 7.325A pdb=" N TYR A 497 " --> pdb=" O PHE A 521 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU A 555 " --> pdb=" O ARG A 540 " (cutoff:3.500A) removed outlier: 5.835A pdb=" N ARG A 540 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N CYS A 557 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N VAL A 538 " --> pdb=" O CYS A 557 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL A 538 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 291 through 294 removed outlier: 5.290A pdb=" N ASP A 494 " --> pdb=" O VAL A 485 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL A 485 " --> pdb=" O ASP A 494 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU A 496 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ASN A 483 " --> pdb=" O LEU A 496 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 498 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LYS A 477 " --> pdb=" O LYS A 502 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR A 476 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 374 removed outlier: 5.966A pdb=" N GLN A 373 " --> pdb=" O LYS B 365 " (cutoff:3.500A) removed outlier: 8.515A pdb=" N GLN B 367 " --> pdb=" O GLN A 373 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 625 through 627 removed outlier: 7.066A pdb=" N VAL A 625 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN B 2 " --> pdb=" O THR A 619 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 54 through 57 Processing sheet with id=AA7, first strand: chain 'B' and resid 128 through 130 removed outlier: 3.564A pdb=" N ARG B 135 " --> pdb=" O ASP B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 179 through 184 Processing sheet with id=AA9, first strand: chain 'B' and resid 240 through 244 removed outlier: 6.938A pdb=" N LEU B 224 " --> pdb=" O ARG B 350 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 488 through 491 Processing sheet with id=AB2, first strand: chain 'B' and resid 641 through 642 removed outlier: 4.101A pdb=" N ALA B 642 " --> pdb=" O MET B 654 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET B 654 " --> pdb=" O ALA B 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 455 hydrogen bonds defined for protein. 1290 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 16 hydrogen bonds 32 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 4.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2394 1.33 - 1.45: 2340 1.45 - 1.57: 5907 1.57 - 1.69: 47 1.69 - 1.81: 133 Bond restraints: 10821 Sorted by residual: bond pdb=" N ASP B 445 " pdb=" CA ASP B 445 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.21e-02 6.83e+03 8.55e+00 bond pdb=" N LYS A 300 " pdb=" CA LYS A 300 " ideal model delta sigma weight residual 1.456 1.487 -0.030 1.16e-02 7.43e+03 6.84e+00 bond pdb=" N PHE B 446 " pdb=" CA PHE B 446 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.23e-02 6.61e+03 6.75e+00 bond pdb=" N ASP B 444 " pdb=" CA ASP B 444 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.27e-02 6.20e+03 6.49e+00 bond pdb=" N LYS A 301 " pdb=" CA LYS A 301 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.41e-02 5.03e+03 6.28e+00 ... (remaining 10816 not shown) Histogram of bond angle deviations from ideal: 98.75 - 105.83: 371 105.83 - 112.91: 5724 112.91 - 119.99: 3950 119.99 - 127.07: 4501 127.07 - 134.15: 169 Bond angle restraints: 14715 Sorted by residual: angle pdb=" N LYS B 393 " pdb=" CA LYS B 393 " pdb=" C LYS B 393 " ideal model delta sigma weight residual 109.81 119.58 -9.77 2.21e+00 2.05e-01 1.95e+01 angle pdb=" N ILE B 339 " pdb=" CA ILE B 339 " pdb=" C ILE B 339 " ideal model delta sigma weight residual 112.12 108.89 3.23 8.40e-01 1.42e+00 1.48e+01 angle pdb=" CA TRP B 437 " pdb=" CB TRP B 437 " pdb=" CG TRP B 437 " ideal model delta sigma weight residual 113.60 120.80 -7.20 1.90e+00 2.77e-01 1.44e+01 angle pdb=" C ILE B 427 " pdb=" N LYS B 428 " pdb=" CA LYS B 428 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N GLY A 542 " pdb=" CA GLY A 542 " pdb=" C GLY A 542 " ideal model delta sigma weight residual 110.58 115.27 -4.69 1.35e+00 5.49e-01 1.21e+01 ... (remaining 14710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 5859 17.31 - 34.61: 538 34.61 - 51.92: 128 51.92 - 69.22: 59 69.22 - 86.53: 16 Dihedral angle restraints: 6600 sinusoidal: 2943 harmonic: 3657 Sorted by residual: dihedral pdb=" CA MET B 409 " pdb=" C MET B 409 " pdb=" N MET B 410 " pdb=" CA MET B 410 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA MET B 408 " pdb=" C MET B 408 " pdb=" N MET B 409 " pdb=" CA MET B 409 " ideal model delta harmonic sigma weight residual 180.00 159.03 20.97 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA THR B 303 " pdb=" C THR B 303 " pdb=" N GLY B 304 " pdb=" CA GLY B 304 " ideal model delta harmonic sigma weight residual -180.00 -161.33 -18.67 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 6597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1100 0.050 - 0.101: 450 0.101 - 0.151: 78 0.151 - 0.201: 7 0.201 - 0.252: 2 Chirality restraints: 1637 Sorted by residual: chirality pdb=" CB VAL A 485 " pdb=" CA VAL A 485 " pdb=" CG1 VAL A 485 " pdb=" CG2 VAL A 485 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CB VAL A 277 " pdb=" CA VAL A 277 " pdb=" CG1 VAL A 277 " pdb=" CG2 VAL A 277 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA LYS B 393 " pdb=" N LYS B 393 " pdb=" C LYS B 393 " pdb=" CB LYS B 393 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.93e-01 ... (remaining 1634 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A V 4 " 0.034 2.00e-02 2.50e+03 1.53e-02 6.40e+00 pdb=" N9 A V 4 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A V 4 " -0.006 2.00e-02 2.50e+03 pdb=" N7 A V 4 " 0.006 2.00e-02 2.50e+03 pdb=" C5 A V 4 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 4 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A V 4 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A V 4 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A V 4 " -0.003 2.00e-02 2.50e+03 pdb=" N3 A V 4 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A V 4 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 137 " 0.041 5.00e-02 4.00e+02 6.25e-02 6.25e+00 pdb=" N PRO B 138 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 138 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 138 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 314 " 0.037 5.00e-02 4.00e+02 5.65e-02 5.11e+00 pdb=" N PRO B 315 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO B 315 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO B 315 " 0.031 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2449 2.78 - 3.31: 8765 3.31 - 3.84: 17233 3.84 - 4.37: 20970 4.37 - 4.90: 36206 Nonbonded interactions: 85623 Sorted by model distance: nonbonded pdb=" OD2 ASP B 521 " pdb=" OH TYR B 558 " model vdw 2.251 2.440 nonbonded pdb=" O ILE B 18 " pdb=" OG1 THR B 21 " model vdw 2.283 2.440 nonbonded pdb=" O LEU A 211 " pdb=" OG SER A 215 " model vdw 2.286 2.440 nonbonded pdb=" O SER B 291 " pdb=" OG SER B 291 " model vdw 2.305 2.440 nonbonded pdb=" O ALA A 362 " pdb=" OG1 THR A 366 " model vdw 2.311 2.440 ... (remaining 85618 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.850 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 32.890 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.008 0.072 10821 Z= 0.515 Angle : 0.803 9.768 14715 Z= 0.459 Chirality : 0.052 0.252 1637 Planarity : 0.007 0.063 1796 Dihedral : 15.458 86.528 4248 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.63 % Favored : 94.29 % Rotamer: Outliers : 6.26 % Allowed : 8.17 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -3.70 (0.18), residues: 1260 helix: -2.29 (0.16), residues: 548 sheet: -1.83 (0.37), residues: 151 loop : -2.71 (0.22), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP B 437 HIS 0.006 0.001 HIS A 462 PHE 0.015 0.002 PHE B 181 TYR 0.020 0.003 TYR A 644 ARG 0.006 0.001 ARG B 233 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 171 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 231 ASP cc_start: 0.7665 (m-30) cc_final: 0.7438 (t0) REVERT: A 261 ASP cc_start: 0.7393 (m-30) cc_final: 0.7191 (m-30) REVERT: A 373 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8007 (pt0) REVERT: A 437 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7437 (mp0) REVERT: A 508 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7499 (mtp180) REVERT: B 196 ARG cc_start: 0.2403 (OUTLIER) cc_final: 0.1864 (mtt180) REVERT: B 273 VAL cc_start: 0.5345 (OUTLIER) cc_final: 0.5137 (p) REVERT: B 279 LYS cc_start: 0.6822 (mttt) cc_final: 0.6569 (mptt) REVERT: B 314 ASN cc_start: 0.8123 (OUTLIER) cc_final: 0.7876 (m-40) REVERT: B 380 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8274 (mtm180) REVERT: B 570 LYS cc_start: 0.8100 (mttt) cc_final: 0.7782 (mtmm) REVERT: B 641 GLU cc_start: 0.3486 (OUTLIER) cc_final: 0.1952 (mp0) REVERT: C 120 PHE cc_start: 0.4881 (OUTLIER) cc_final: 0.4622 (m-80) outliers start: 69 outliers final: 31 residues processed: 233 average time/residue: 0.2453 time to fit residues: 78.9587 Evaluate side-chains 169 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 129 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 339 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 373 GLN Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 431 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 472 SER Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 625 VAL Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 86 ASP Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 273 VAL Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 329 SER Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain C residue 120 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 20.0000 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 116 optimal weight: 8.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 467 ASN A 666 GLN B 47 HIS B 70 ASN B 99 HIS B 104 GLN ** B 268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 306 ASN B 314 ASN B 367 GLN B 548 GLN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 ASN C 68 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10821 Z= 0.197 Angle : 0.527 7.988 14715 Z= 0.281 Chirality : 0.040 0.187 1637 Planarity : 0.005 0.049 1796 Dihedral : 13.010 73.841 1810 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 3.36 % Allowed : 12.89 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.21), residues: 1260 helix: -0.19 (0.20), residues: 553 sheet: -1.69 (0.38), residues: 154 loop : -2.16 (0.23), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 437 HIS 0.002 0.000 HIS B 47 PHE 0.012 0.001 PHE B 489 TYR 0.011 0.001 TYR B 554 ARG 0.002 0.000 ARG B 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.215 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7411 (mtp180) REVERT: B 15 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.7944 (mp10) REVERT: B 124 GLN cc_start: 0.7416 (mm-40) cc_final: 0.7178 (mp10) REVERT: B 380 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8195 (mtm180) REVERT: B 570 LYS cc_start: 0.8103 (mttt) cc_final: 0.7747 (mtmm) REVERT: B 641 GLU cc_start: 0.3488 (OUTLIER) cc_final: 0.1973 (mp0) REVERT: C 92 MET cc_start: 0.7779 (mmt) cc_final: 0.7281 (mmt) outliers start: 37 outliers final: 23 residues processed: 158 average time/residue: 0.2201 time to fit residues: 49.9700 Evaluate side-chains 153 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 397 ASN Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 533 MET Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain C residue 125 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 7.9990 chunk 36 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 125 optimal weight: 8.9990 chunk 103 optimal weight: 0.0010 chunk 115 optimal weight: 0.0570 chunk 39 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 overall best weight: 2.6110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 10821 Z= 0.249 Angle : 0.512 7.700 14715 Z= 0.270 Chirality : 0.041 0.161 1637 Planarity : 0.004 0.042 1796 Dihedral : 12.279 73.876 1775 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 3.36 % Allowed : 13.88 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.22), residues: 1260 helix: 0.64 (0.22), residues: 554 sheet: -1.50 (0.39), residues: 148 loop : -1.88 (0.24), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 437 HIS 0.002 0.001 HIS A 506 PHE 0.011 0.001 PHE B 489 TYR 0.011 0.001 TYR B 381 ARG 0.003 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 129 time to evaluate : 1.234 Fit side-chains revert: symmetry clash REVERT: A 261 ASP cc_start: 0.7613 (m-30) cc_final: 0.7383 (m-30) REVERT: A 373 GLN cc_start: 0.8377 (pt0) cc_final: 0.8082 (pt0) REVERT: A 424 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8512 (pt) REVERT: A 437 GLU cc_start: 0.7458 (OUTLIER) cc_final: 0.6407 (mp0) REVERT: A 508 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7386 (mtp180) REVERT: A 599 MET cc_start: 0.5194 (mpp) cc_final: 0.4501 (mtp) REVERT: B 15 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.7957 (mp10) REVERT: B 279 LYS cc_start: 0.7010 (mttt) cc_final: 0.6505 (mptt) REVERT: B 380 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8398 (mtm180) REVERT: B 570 LYS cc_start: 0.8084 (mttt) cc_final: 0.7723 (mtmm) outliers start: 37 outliers final: 25 residues processed: 156 average time/residue: 0.2383 time to fit residues: 52.9851 Evaluate side-chains 154 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 124 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 641 GLU Chi-restraints excluded: chain C residue 125 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 123 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10821 Z= 0.262 Angle : 0.516 7.626 14715 Z= 0.269 Chirality : 0.041 0.177 1637 Planarity : 0.004 0.039 1796 Dihedral : 12.083 73.790 1768 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.57 % Favored : 96.35 % Rotamer: Outliers : 3.27 % Allowed : 15.43 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.80 (0.23), residues: 1260 helix: 0.91 (0.22), residues: 554 sheet: -1.41 (0.39), residues: 144 loop : -1.78 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 437 HIS 0.003 0.001 HIS A 506 PHE 0.010 0.001 PHE B 489 TYR 0.012 0.001 TYR B 554 ARG 0.004 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 1.260 Fit side-chains REVERT: A 261 ASP cc_start: 0.7638 (m-30) cc_final: 0.7413 (m-30) REVERT: A 373 GLN cc_start: 0.8408 (pt0) cc_final: 0.8104 (pt0) REVERT: A 424 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8521 (pt) REVERT: A 437 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6415 (mp0) REVERT: A 599 MET cc_start: 0.5140 (mpp) cc_final: 0.4428 (mtp) REVERT: B 15 GLN cc_start: 0.8963 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: B 380 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8411 (mtm180) REVERT: B 570 LYS cc_start: 0.8069 (mttt) cc_final: 0.7721 (mtmm) REVERT: C 53 MET cc_start: 0.7734 (mmp) cc_final: 0.7533 (mmm) REVERT: C 92 MET cc_start: 0.7844 (mmt) cc_final: 0.7463 (mmt) outliers start: 36 outliers final: 27 residues processed: 152 average time/residue: 0.2159 time to fit residues: 47.4528 Evaluate side-chains 152 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 200 ILE Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain A residue 684 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 113 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 186 ASN Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 440 LEU Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 533 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 0.0570 chunk 70 optimal weight: 0.0060 chunk 1 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 105 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 0.7516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10821 Z= 0.117 Angle : 0.448 8.201 14715 Z= 0.234 Chirality : 0.038 0.139 1637 Planarity : 0.003 0.038 1796 Dihedral : 11.741 73.689 1760 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 2.18 % Allowed : 16.61 % Favored : 81.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.23), residues: 1260 helix: 1.38 (0.22), residues: 556 sheet: -1.01 (0.41), residues: 132 loop : -1.54 (0.24), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 437 HIS 0.002 0.000 HIS A 272 PHE 0.007 0.001 PHE A 223 TYR 0.011 0.001 TYR B 556 ARG 0.002 0.000 ARG B 666 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.321 Fit side-chains REVERT: A 261 ASP cc_start: 0.7580 (m-30) cc_final: 0.7372 (m-30) REVERT: A 373 GLN cc_start: 0.8367 (pt0) cc_final: 0.8026 (pt0) REVERT: A 437 GLU cc_start: 0.7373 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: A 485 VAL cc_start: 0.8844 (OUTLIER) cc_final: 0.8632 (m) REVERT: A 508 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7408 (mtp180) REVERT: A 590 GLN cc_start: 0.7583 (mm110) cc_final: 0.6956 (mm110) REVERT: A 599 MET cc_start: 0.5113 (mpp) cc_final: 0.4382 (mtp) REVERT: B 15 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7835 (mp10) REVERT: B 380 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8340 (mtm180) REVERT: B 570 LYS cc_start: 0.8031 (mttt) cc_final: 0.7682 (mtmm) REVERT: C 92 MET cc_start: 0.7955 (mmt) cc_final: 0.7526 (mmt) outliers start: 24 outliers final: 15 residues processed: 149 average time/residue: 0.2364 time to fit residues: 49.9745 Evaluate side-chains 143 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 485 VAL Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 533 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 5.9990 chunk 111 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 30 optimal weight: 0.0870 chunk 123 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 57 optimal weight: 0.0370 chunk 10 optimal weight: 10.0000 chunk 40 optimal weight: 10.0000 chunk 65 optimal weight: 2.9990 overall best weight: 2.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 ASN B 292 ASN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10821 Z= 0.202 Angle : 0.476 7.122 14715 Z= 0.248 Chirality : 0.040 0.153 1637 Planarity : 0.004 0.036 1796 Dihedral : 11.689 73.798 1754 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.02 % Favored : 96.90 % Rotamer: Outliers : 2.81 % Allowed : 16.79 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: -0.17 (0.23), residues: 1260 helix: 1.45 (0.22), residues: 557 sheet: -1.06 (0.40), residues: 144 loop : -1.49 (0.24), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 437 HIS 0.002 0.001 HIS A 506 PHE 0.008 0.001 PHE B 489 TYR 0.012 0.001 TYR B 554 ARG 0.004 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 127 time to evaluate : 1.280 Fit side-chains REVERT: A 261 ASP cc_start: 0.7597 (m-30) cc_final: 0.7385 (m-30) REVERT: A 373 GLN cc_start: 0.8398 (pt0) cc_final: 0.8025 (pt0) REVERT: A 437 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.6378 (mp0) REVERT: A 508 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7317 (mtp180) REVERT: A 590 GLN cc_start: 0.7668 (mm110) cc_final: 0.7048 (mm110) REVERT: A 599 MET cc_start: 0.5077 (mpp) cc_final: 0.4361 (mtp) REVERT: B 15 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: B 95 MET cc_start: 0.8744 (ttm) cc_final: 0.8370 (ttp) REVERT: B 282 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7444 (mp) REVERT: B 380 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8322 (mtm180) REVERT: B 528 ILE cc_start: 0.9221 (OUTLIER) cc_final: 0.8998 (mt) REVERT: B 570 LYS cc_start: 0.8078 (mttt) cc_final: 0.7711 (mtmm) REVERT: C 92 MET cc_start: 0.7984 (mmt) cc_final: 0.7553 (mmt) outliers start: 31 outliers final: 21 residues processed: 152 average time/residue: 0.2285 time to fit residues: 49.2864 Evaluate side-chains 148 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain B residue 533 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 70 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10821 Z= 0.215 Angle : 0.493 9.792 14715 Z= 0.254 Chirality : 0.040 0.154 1637 Planarity : 0.004 0.037 1796 Dihedral : 11.706 73.835 1754 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.18 % Allowed : 16.88 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 (0.23), residues: 1260 helix: 1.42 (0.22), residues: 556 sheet: -0.99 (0.40), residues: 144 loop : -1.44 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 437 HIS 0.002 0.000 HIS A 272 PHE 0.008 0.001 PHE B 489 TYR 0.012 0.001 TYR B 554 ARG 0.003 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 1.194 Fit side-chains REVERT: A 261 ASP cc_start: 0.7600 (m-30) cc_final: 0.7389 (m-30) REVERT: A 437 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.6337 (mp0) REVERT: A 508 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7367 (mtp180) REVERT: A 590 GLN cc_start: 0.7664 (mm110) cc_final: 0.7089 (mm110) REVERT: A 599 MET cc_start: 0.5065 (mpp) cc_final: 0.4355 (mtp) REVERT: B 15 GLN cc_start: 0.8947 (OUTLIER) cc_final: 0.7920 (mp10) REVERT: B 95 MET cc_start: 0.8752 (ttm) cc_final: 0.8387 (ttp) REVERT: B 196 ARG cc_start: 0.2631 (OUTLIER) cc_final: 0.2016 (mtt180) REVERT: B 282 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7471 (mp) REVERT: B 380 ARG cc_start: 0.9010 (OUTLIER) cc_final: 0.8352 (mtm180) REVERT: B 570 LYS cc_start: 0.8095 (mttt) cc_final: 0.7727 (mtmm) outliers start: 35 outliers final: 26 residues processed: 151 average time/residue: 0.2620 time to fit residues: 56.0624 Evaluate side-chains 152 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 120 time to evaluate : 1.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain B residue 533 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 84 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 0.3980 chunk 112 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 195 ASN B 292 ASN ** C 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10821 Z= 0.146 Angle : 0.464 10.829 14715 Z= 0.240 Chirality : 0.039 0.166 1637 Planarity : 0.003 0.036 1796 Dihedral : 11.639 73.789 1754 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.45 % Allowed : 17.79 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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: 0.03 (0.24), residues: 1260 helix: 1.57 (0.22), residues: 557 sheet: -0.67 (0.43), residues: 132 loop : -1.42 (0.24), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 437 HIS 0.001 0.000 HIS A 272 PHE 0.007 0.001 PHE B 489 TYR 0.011 0.001 TYR B 554 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 126 time to evaluate : 1.183 Fit side-chains REVERT: A 261 ASP cc_start: 0.7577 (m-30) cc_final: 0.7376 (m-30) REVERT: A 373 GLN cc_start: 0.8422 (pt0) cc_final: 0.8049 (pt0) REVERT: A 437 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.6343 (mp0) REVERT: A 508 ARG cc_start: 0.7949 (OUTLIER) cc_final: 0.7386 (mtp180) REVERT: A 590 GLN cc_start: 0.7636 (mm110) cc_final: 0.7075 (mm110) REVERT: A 599 MET cc_start: 0.5058 (mpp) cc_final: 0.4317 (mtp) REVERT: B 15 GLN cc_start: 0.8914 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: B 95 MET cc_start: 0.8750 (ttm) cc_final: 0.8375 (ttp) REVERT: B 196 ARG cc_start: 0.2660 (OUTLIER) cc_final: 0.2035 (mtt180) REVERT: B 282 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7358 (mp) REVERT: B 380 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8390 (mtm180) REVERT: B 570 LYS cc_start: 0.8105 (mttt) cc_final: 0.7714 (mtmm) REVERT: C 92 MET cc_start: 0.7847 (mmt) cc_final: 0.7589 (mmt) outliers start: 27 outliers final: 21 residues processed: 148 average time/residue: 0.2363 time to fit residues: 49.7661 Evaluate side-chains 145 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 436 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 103 optimal weight: 10.0000 chunk 108 optimal weight: 0.9990 chunk 75 optimal weight: 7.9990 chunk 121 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10821 Z= 0.185 Angle : 0.486 12.275 14715 Z= 0.250 Chirality : 0.040 0.157 1637 Planarity : 0.003 0.036 1796 Dihedral : 11.616 73.886 1753 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.81 % Allowed : 17.70 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % 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 (0.23), residues: 1260 helix: 1.52 (0.22), residues: 557 sheet: -0.56 (0.41), residues: 141 loop : -1.47 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 437 HIS 0.001 0.000 HIS A 272 PHE 0.008 0.001 PHE B 489 TYR 0.013 0.001 TYR B 30 ARG 0.004 0.000 ARG B 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.209 Fit side-chains REVERT: A 261 ASP cc_start: 0.7599 (m-30) cc_final: 0.7383 (m-30) REVERT: A 437 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6340 (mp0) REVERT: A 508 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7364 (mtp180) REVERT: A 590 GLN cc_start: 0.7678 (mm110) cc_final: 0.7127 (mm110) REVERT: A 599 MET cc_start: 0.5062 (mpp) cc_final: 0.4346 (mtp) REVERT: B 15 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.7872 (mp10) REVERT: B 95 MET cc_start: 0.8749 (ttm) cc_final: 0.8379 (ttp) REVERT: B 196 ARG cc_start: 0.2662 (OUTLIER) cc_final: 0.2040 (mtt180) REVERT: B 282 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7390 (mp) REVERT: B 380 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8398 (mtm180) REVERT: B 570 LYS cc_start: 0.8119 (mttt) cc_final: 0.7717 (mtmm) REVERT: C 92 MET cc_start: 0.7841 (mmt) cc_final: 0.7576 (mmt) outliers start: 31 outliers final: 25 residues processed: 146 average time/residue: 0.2284 time to fit residues: 47.4059 Evaluate side-chains 149 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 118 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 483 CYS Chi-restraints excluded: chain B residue 490 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 3.9990 chunk 57 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 117 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 10 optimal weight: 10.0000 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 0.6980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10821 Z= 0.181 Angle : 0.484 12.630 14715 Z= 0.249 Chirality : 0.040 0.183 1637 Planarity : 0.003 0.036 1796 Dihedral : 11.606 73.776 1753 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.81 % Allowed : 17.51 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1260 helix: 1.56 (0.22), residues: 557 sheet: -0.54 (0.41), residues: 141 loop : -1.46 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 437 HIS 0.001 0.000 HIS B 32 PHE 0.007 0.001 PHE B 489 TYR 0.013 0.001 TYR B 30 ARG 0.004 0.000 ARG B 135 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2520 Ramachandran restraints generated. 1260 Oldfield, 0 Emsley, 1260 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 123 time to evaluate : 1.206 Fit side-chains REVERT: A 261 ASP cc_start: 0.7594 (m-30) cc_final: 0.7381 (m-30) REVERT: A 437 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6341 (mp0) REVERT: A 508 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7365 (mtp180) REVERT: A 590 GLN cc_start: 0.7668 (mm110) cc_final: 0.7135 (mm110) REVERT: A 599 MET cc_start: 0.5087 (mpp) cc_final: 0.4393 (mtp) REVERT: B 15 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7879 (mp10) REVERT: B 95 MET cc_start: 0.8748 (ttm) cc_final: 0.8380 (ttp) REVERT: B 196 ARG cc_start: 0.2660 (OUTLIER) cc_final: 0.2036 (mtt180) REVERT: B 282 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7377 (mp) REVERT: B 380 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8434 (mtm180) REVERT: B 570 LYS cc_start: 0.8119 (mttt) cc_final: 0.7716 (mtmm) REVERT: C 92 MET cc_start: 0.7839 (mmt) cc_final: 0.7577 (mmt) outliers start: 31 outliers final: 25 residues processed: 148 average time/residue: 0.2383 time to fit residues: 50.1724 Evaluate side-chains 152 residues out of total 1102 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 257 LEU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 395 ASN Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 437 GLU Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 508 ARG Chi-restraints excluded: chain A residue 515 THR Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 557 CYS Chi-restraints excluded: chain A residue 617 ILE Chi-restraints excluded: chain A residue 619 THR Chi-restraints excluded: chain A residue 628 SER Chi-restraints excluded: chain B residue 15 GLN Chi-restraints excluded: chain B residue 32 HIS Chi-restraints excluded: chain B residue 41 ASP Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 314 ASN Chi-restraints excluded: chain B residue 337 CYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 361 THR Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 483 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 0.0000 chunk 93 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.0770 chunk 89 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 overall best weight: 1.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.151283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.118486 restraints weight = 13057.647| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.58 r_work: 0.3062 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10821 Z= 0.174 Angle : 0.480 12.311 14715 Z= 0.246 Chirality : 0.040 0.180 1637 Planarity : 0.003 0.036 1796 Dihedral : 11.596 73.766 1753 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.90 % Allowed : 17.60 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.24), residues: 1260 helix: 1.59 (0.22), residues: 557 sheet: -0.51 (0.41), residues: 141 loop : -1.45 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 437 HIS 0.001 0.000 HIS A 272 PHE 0.008 0.001 PHE B 489 TYR 0.012 0.001 TYR B 30 ARG 0.004 0.000 ARG B 135 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2328.23 seconds wall clock time: 43 minutes 0.38 seconds (2580.38 seconds total)