Starting phenix.real_space_refine on Sun Aug 4 16:35:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvy_38723/08_2024/8xvy_38723.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvy_38723/08_2024/8xvy_38723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvy_38723/08_2024/8xvy_38723.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvy_38723/08_2024/8xvy_38723.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvy_38723/08_2024/8xvy_38723.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xvy_38723/08_2024/8xvy_38723.cif" } resolution = 3.71 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= 0.008 sd= 0.059 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 7254 2.51 5 N 1737 2.21 5 O 1893 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 178": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 241": "OE1" <-> "OE2" Residue "B ARG 263": "NH1" <-> "NH2" Residue "B GLU 343": "OE1" <-> "OE2" Residue "B GLU 414": "OE1" <-> "OE2" Residue "B GLU 440": "OE1" <-> "OE2" Residue "B GLU 541": "OE1" <-> "OE2" Residue "B GLU 607": "OE1" <-> "OE2" Residue "B TYR 642": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 56": "NH1" <-> "NH2" Residue "A ARG 178": "NH1" <-> "NH2" Residue "A GLU 232": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "A ARG 263": "NH1" <-> "NH2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 296": "OE1" <-> "OE2" Residue "A ARG 395": "NH1" <-> "NH2" Residue "A ARG 410": "NH1" <-> "NH2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A GLU 541": "OE1" <-> "OE2" Residue "A PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10923 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 687, 5512 Classifications: {'peptide': 687} Link IDs: {'PTRANS': 31, 'TRANS': 655} Chain breaks: 1 Chain: "A" Number of atoms: 5411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 674, 5411 Classifications: {'peptide': 674} Link IDs: {'PTRANS': 30, 'TRANS': 643} Chain breaks: 2 Time building chain proxies: 6.03, per 1000 atoms: 0.55 Number of scatterers: 10923 At special positions: 0 Unit cell: (86.51, 142.425, 102.335, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1893 8.00 N 1737 7.00 C 7254 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: 4.70 Conformation dependent library (CDL) restraints added in 2.2 seconds 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2602 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 3 sheets defined 70.4% alpha, 3.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'B' and resid 2 through 28 Processing helix chain 'B' and resid 29 through 32 removed outlier: 6.710A pdb=" N GLY B 32 " --> pdb=" O ARG B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 32' Processing helix chain 'B' and resid 33 through 38 Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 61 through 67 removed outlier: 3.722A pdb=" N THR B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 77 Processing helix chain 'B' and resid 78 through 113 removed outlier: 3.900A pdb=" N ALA B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL B 83 " --> pdb=" O VAL B 79 " (cutoff:3.500A) Proline residue: B 104 - end of helix Proline residue: B 108 - end of helix Processing helix chain 'B' and resid 132 through 137 Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.671A pdb=" N ASN B 141 " --> pdb=" O SER B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 183 removed outlier: 3.778A pdb=" N ALA B 151 " --> pdb=" O SER B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 191 Processing helix chain 'B' and resid 207 through 213 Processing helix chain 'B' and resid 215 through 220 Processing helix chain 'B' and resid 233 through 261 Processing helix chain 'B' and resid 280 through 304 removed outlier: 4.052A pdb=" N ALA B 304 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 327 removed outlier: 3.855A pdb=" N ALA B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B 326 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N SER B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 389 Proline residue: B 380 - end of helix removed outlier: 3.917A pdb=" N THR B 389 " --> pdb=" O SER B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 389 through 396 removed outlier: 3.843A pdb=" N ARG B 395 " --> pdb=" O LYS B 391 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 396 " --> pdb=" O ASN B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 401 Processing helix chain 'B' and resid 406 through 439 removed outlier: 3.867A pdb=" N ARG B 410 " --> pdb=" O ILE B 406 " (cutoff:3.500A) Proline residue: B 418 - end of helix Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 444 through 476 Processing helix chain 'B' and resid 477 through 481 removed outlier: 3.672A pdb=" N ILE B 481 " --> pdb=" O VAL B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 523 removed outlier: 3.618A pdb=" N ILE B 490 " --> pdb=" O LYS B 486 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ILE B 491 " --> pdb=" O LEU B 487 " (cutoff:3.500A) Proline residue: B 499 - end of helix Processing helix chain 'B' and resid 523 through 530 Processing helix chain 'B' and resid 543 through 547 removed outlier: 3.657A pdb=" N GLU B 546 " --> pdb=" O GLU B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 572 removed outlier: 3.593A pdb=" N VAL B 559 " --> pdb=" O TYR B 555 " (cutoff:3.500A) Proline residue: B 560 - end of helix Processing helix chain 'B' and resid 578 through 601 removed outlier: 3.693A pdb=" N PHE B 582 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 635 removed outlier: 3.520A pdb=" N ILE B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 645 Processing helix chain 'B' and resid 646 through 664 Processing helix chain 'B' and resid 665 through 668 Processing helix chain 'A' and resid 2 through 29 removed outlier: 3.624A pdb=" N ARG A 29 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 32 No H-bonds generated for 'chain 'A' and resid 30 through 32' Processing helix chain 'A' and resid 33 through 38 Processing helix chain 'A' and resid 61 through 67 removed outlier: 4.085A pdb=" N ALA A 65 " --> pdb=" O TRP A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 77 Processing helix chain 'A' and resid 78 through 113 removed outlier: 3.828A pdb=" N ALA A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Proline residue: A 104 - end of helix Proline residue: A 108 - end of helix removed outlier: 3.700A pdb=" N ASP A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 137 Processing helix chain 'A' and resid 147 through 185 removed outlier: 3.973A pdb=" N ALA A 151 " --> pdb=" O SER A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 191 Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 233 through 261 Processing helix chain 'A' and resid 279 through 303 removed outlier: 3.570A pdb=" N LEU A 303 " --> pdb=" O GLN A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 355 through 388 Proline residue: A 380 - end of helix Processing helix chain 'A' and resid 388 through 394 removed outlier: 3.756A pdb=" N GLN A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 438 removed outlier: 3.651A pdb=" N ARG A 410 " --> pdb=" O ILE A 406 " (cutoff:3.500A) Proline residue: A 418 - end of helix Proline residue: A 430 - end of helix Processing helix chain 'A' and resid 439 through 441 No H-bonds generated for 'chain 'A' and resid 439 through 441' Processing helix chain 'A' and resid 444 through 476 Processing helix chain 'A' and resid 491 through 523 removed outlier: 3.970A pdb=" N ALA A 495 " --> pdb=" O ILE A 491 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER A 497 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 498 " --> pdb=" O LEU A 494 " (cutoff:3.500A) Proline residue: A 499 - end of helix removed outlier: 3.886A pdb=" N THR A 503 " --> pdb=" O PRO A 499 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 504 " --> pdb=" O LYS A 500 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 510 " --> pdb=" O LEU A 506 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 516 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N TYR A 517 " --> pdb=" O PHE A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 530 Processing helix chain 'A' and resid 543 through 548 Processing helix chain 'A' and resid 554 through 572 Proline residue: A 560 - end of helix Processing helix chain 'A' and resid 578 through 601 removed outlier: 3.860A pdb=" N PHE A 582 " --> pdb=" O LEU A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 638 removed outlier: 3.772A pdb=" N ILE A 616 " --> pdb=" O MET A 612 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 665 removed outlier: 4.023A pdb=" N LEU A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 666 through 669 removed outlier: 3.531A pdb=" N GLU A 669 " --> pdb=" O GLY A 666 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 666 through 669' Processing sheet with id=AA1, first strand: chain 'B' and resid 224 through 229 removed outlier: 3.561A pdb=" N ARG B 226 " --> pdb=" O PHE B 314 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 339 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 265 through 268 Processing sheet with id=AA3, first strand: chain 'A' and resid 224 through 231 removed outlier: 3.613A pdb=" N ARG A 226 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ALA A 310 " --> pdb=" O ALA A 230 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 339 " --> pdb=" O LEU A 195 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1986 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.83 Time building geometry restraints manager: 5.14 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: 1906 1.33 - 1.45: 2920 1.45 - 1.57: 6321 1.57 - 1.69: 0 1.69 - 1.81: 64 Bond restraints: 11211 Sorted by residual: bond pdb=" C GLU B 619 " pdb=" N ILE B 620 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.23e-02 6.61e+03 5.69e+00 bond pdb=" C GLU B 611 " pdb=" O GLU B 611 " ideal model delta sigma weight residual 1.236 1.207 0.029 1.31e-02 5.83e+03 5.00e+00 bond pdb=" CA GLU B 611 " pdb=" C GLU B 611 " ideal model delta sigma weight residual 1.522 1.498 0.024 1.37e-02 5.33e+03 3.19e+00 bond pdb=" N GLU A 619 " pdb=" CA GLU A 619 " ideal model delta sigma weight residual 1.459 1.480 -0.021 1.17e-02 7.31e+03 3.18e+00 bond pdb=" C ILE A 397 " pdb=" N PRO A 398 " ideal model delta sigma weight residual 1.331 1.353 -0.023 1.31e-02 5.83e+03 3.04e+00 ... (remaining 11206 not shown) Histogram of bond angle deviations from ideal: 99.57 - 106.49: 305 106.49 - 113.41: 6137 113.41 - 120.33: 4400 120.33 - 127.25: 4277 127.25 - 134.17: 121 Bond angle restraints: 15240 Sorted by residual: angle pdb=" N THR A 55 " pdb=" CA THR A 55 " pdb=" C THR A 55 " ideal model delta sigma weight residual 114.75 106.02 8.73 1.26e+00 6.30e-01 4.80e+01 angle pdb=" C LEU B 626 " pdb=" N PHE B 627 " pdb=" CA PHE B 627 " ideal model delta sigma weight residual 122.26 115.00 7.26 1.59e+00 3.96e-01 2.08e+01 angle pdb=" CA THR A 55 " pdb=" C THR A 55 " pdb=" N ARG A 56 " ideal model delta sigma weight residual 119.80 114.26 5.54 1.34e+00 5.57e-01 1.71e+01 angle pdb=" C VAL A 646 " pdb=" N ILE A 647 " pdb=" CA ILE A 647 " ideal model delta sigma weight residual 120.24 122.78 -2.54 6.30e-01 2.52e+00 1.62e+01 angle pdb=" N TYR A 377 " pdb=" CA TYR A 377 " pdb=" C TYR A 377 " ideal model delta sigma weight residual 111.24 106.07 5.17 1.29e+00 6.01e-01 1.60e+01 ... (remaining 15235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5960 17.94 - 35.87: 532 35.87 - 53.81: 89 53.81 - 71.74: 17 71.74 - 89.68: 8 Dihedral angle restraints: 6606 sinusoidal: 2586 harmonic: 4020 Sorted by residual: dihedral pdb=" CA PHE B 627 " pdb=" C PHE B 627 " pdb=" N GLN B 628 " pdb=" CA GLN B 628 " ideal model delta harmonic sigma weight residual 180.00 149.76 30.24 0 5.00e+00 4.00e-02 3.66e+01 dihedral pdb=" CA ILE B 42 " pdb=" C ILE B 42 " pdb=" N LEU B 43 " pdb=" CA LEU B 43 " ideal model delta harmonic sigma weight residual 180.00 152.02 27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ILE A 42 " pdb=" C ILE A 42 " pdb=" N LEU A 43 " pdb=" CA LEU A 43 " ideal model delta harmonic sigma weight residual 180.00 153.34 26.66 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 6603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1264 0.044 - 0.088: 388 0.088 - 0.131: 96 0.131 - 0.175: 14 0.175 - 0.219: 5 Chirality restraints: 1767 Sorted by residual: chirality pdb=" CA PHE B 627 " pdb=" N PHE B 627 " pdb=" C PHE B 627 " pdb=" CB PHE B 627 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE A 381 " pdb=" CA ILE A 381 " pdb=" CG1 ILE A 381 " pdb=" CG2 ILE A 381 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CG LEU B 624 " pdb=" CB LEU B 624 " pdb=" CD1 LEU B 624 " pdb=" CD2 LEU B 624 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 1764 not shown) Planarity restraints: 1864 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 171 " 0.025 2.00e-02 2.50e+03 2.13e-02 9.12e+00 pdb=" CG TYR B 171 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR B 171 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 171 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR B 171 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 171 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 171 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 171 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 47 " -0.048 5.00e-02 4.00e+02 7.42e-02 8.80e+00 pdb=" N PRO A 48 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO A 48 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 48 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 610 " 0.015 2.00e-02 2.50e+03 2.91e-02 8.47e+00 pdb=" C GLY B 610 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY B 610 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU B 611 " 0.017 2.00e-02 2.50e+03 ... (remaining 1861 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 229 2.68 - 3.24: 11755 3.24 - 3.79: 17465 3.79 - 4.35: 22451 4.35 - 4.90: 36106 Nonbonded interactions: 88006 Sorted by model distance: nonbonded pdb=" OD2 ASP B 80 " pdb=" OG SER B 608 " model vdw 2.128 3.040 nonbonded pdb=" OH TYR B 215 " pdb=" OE2 GLU A 674 " model vdw 2.129 3.040 nonbonded pdb=" O PHE A 504 " pdb=" OG1 THR A 507 " model vdw 2.186 3.040 nonbonded pdb=" OD2 ASP A 80 " pdb=" OG SER A 608 " model vdw 2.193 3.040 nonbonded pdb=" OE2 GLU B 674 " pdb=" OH TYR A 215 " model vdw 2.193 3.040 ... (remaining 88001 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 1 through 476 or resid 490 through 696)) } 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 group one per residue 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: 1.440 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 33.460 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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 : 0.004 0.042 11211 Z= 0.263 Angle : 0.805 9.044 15240 Z= 0.470 Chirality : 0.045 0.219 1767 Planarity : 0.005 0.074 1864 Dihedral : 14.036 89.679 4004 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.17 % Allowed : 0.59 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.57 (0.23), residues: 1351 helix: 0.59 (0.18), residues: 873 sheet: -3.24 (0.94), residues: 32 loop : -2.07 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 613 HIS 0.006 0.001 HIS A 447 PHE 0.036 0.002 PHE B 513 TYR 0.053 0.002 TYR B 171 ARG 0.009 0.001 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 235 time to evaluate : 1.266 Fit side-chains revert: symmetry clash REVERT: B 27 LEU cc_start: 0.8908 (tp) cc_final: 0.8529 (tp) REVERT: B 198 ASP cc_start: 0.7995 (t0) cc_final: 0.7596 (t0) REVERT: B 378 MET cc_start: 0.8484 (tpt) cc_final: 0.8173 (tpp) REVERT: B 437 SER cc_start: 0.9426 (t) cc_final: 0.9174 (t) REVERT: B 522 SER cc_start: 0.9417 (p) cc_final: 0.9213 (p) REVERT: B 658 TYR cc_start: 0.8388 (t80) cc_final: 0.8055 (t80) REVERT: A 1 MET cc_start: 0.6490 (mmp) cc_final: 0.5745 (ttt) REVERT: A 250 LEU cc_start: 0.9356 (tt) cc_final: 0.8927 (pp) REVERT: A 308 GLN cc_start: 0.8058 (mm110) cc_final: 0.7591 (mm-40) REVERT: A 459 PHE cc_start: 0.7970 (t80) cc_final: 0.7678 (t80) REVERT: A 571 CYS cc_start: 0.9270 (t) cc_final: 0.8994 (t) REVERT: A 619 GLU cc_start: 0.6263 (OUTLIER) cc_final: 0.5700 (mp0) outliers start: 2 outliers final: 0 residues processed: 236 average time/residue: 0.1947 time to fit residues: 70.4242 Evaluate side-chains 182 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 181 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 619 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 54 optimal weight: 0.0000 chunk 105 optimal weight: 20.0000 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 615 HIS ** B 628 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 447 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11211 Z= 0.231 Angle : 0.719 13.823 15240 Z= 0.369 Chirality : 0.045 0.210 1767 Planarity : 0.005 0.058 1864 Dihedral : 5.851 59.910 1469 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.66 % Favored : 91.34 % Rotamer: Outliers : 1.35 % Allowed : 9.81 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.24), residues: 1351 helix: 0.69 (0.18), residues: 888 sheet: -2.95 (1.35), residues: 17 loop : -1.84 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 613 HIS 0.005 0.001 HIS A 615 PHE 0.045 0.002 PHE B 627 TYR 0.039 0.002 TYR A 377 ARG 0.005 0.001 ARG A 558 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 217 time to evaluate : 1.304 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 3 PHE cc_start: 0.6730 (OUTLIER) cc_final: 0.6375 (m-10) REVERT: B 27 LEU cc_start: 0.8975 (tp) cc_final: 0.8687 (tp) REVERT: B 198 ASP cc_start: 0.7768 (t0) cc_final: 0.7069 (t70) REVERT: B 378 MET cc_start: 0.8590 (tpt) cc_final: 0.8186 (tpp) REVERT: B 563 MET cc_start: 0.8963 (mmm) cc_final: 0.8730 (mmm) REVERT: A 1 MET cc_start: 0.6854 (mmp) cc_final: 0.6087 (ttt) REVERT: A 100 LEU cc_start: 0.8475 (mt) cc_final: 0.8165 (mp) REVERT: A 198 ASP cc_start: 0.8209 (m-30) cc_final: 0.7902 (m-30) REVERT: A 250 LEU cc_start: 0.9313 (tt) cc_final: 0.8930 (pp) REVERT: A 308 GLN cc_start: 0.8046 (mm110) cc_final: 0.7383 (mm-40) REVERT: A 361 ILE cc_start: 0.8452 (tt) cc_final: 0.7958 (mm) REVERT: A 364 TYR cc_start: 0.8073 (m-80) cc_final: 0.7852 (m-80) REVERT: A 521 LEU cc_start: 0.9351 (tt) cc_final: 0.9150 (tt) REVERT: A 571 CYS cc_start: 0.9171 (t) cc_final: 0.8905 (t) REVERT: A 640 PHE cc_start: 0.5707 (t80) cc_final: 0.5495 (t80) REVERT: A 669 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7995 (mt-10) outliers start: 16 outliers final: 9 residues processed: 221 average time/residue: 0.1857 time to fit residues: 63.7793 Evaluate side-chains 211 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 201 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 619 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 30.0000 chunk 38 optimal weight: 0.0970 chunk 102 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 121 optimal weight: 0.0270 chunk 41 optimal weight: 0.7980 chunk 98 optimal weight: 0.9980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 ASN B 628 GLN ** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11211 Z= 0.186 Angle : 0.677 12.953 15240 Z= 0.346 Chirality : 0.044 0.193 1767 Planarity : 0.005 0.050 1864 Dihedral : 5.642 59.807 1469 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.95 % Allowed : 13.87 % Favored : 84.18 % 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 (0.24), residues: 1351 helix: 0.82 (0.18), residues: 884 sheet: -3.53 (1.82), residues: 10 loop : -1.67 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 613 HIS 0.004 0.001 HIS A 615 PHE 0.044 0.002 PHE B 627 TYR 0.022 0.002 TYR B 171 ARG 0.003 0.000 ARG B 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 225 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: B 3 PHE cc_start: 0.6405 (OUTLIER) cc_final: 0.6143 (m-80) REVERT: B 27 LEU cc_start: 0.8911 (tp) cc_final: 0.8671 (tp) REVERT: B 171 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.9049 (t80) REVERT: B 198 ASP cc_start: 0.7557 (t0) cc_final: 0.6808 (t70) REVERT: B 563 MET cc_start: 0.9052 (mmm) cc_final: 0.8518 (mmm) REVERT: A 1 MET cc_start: 0.6948 (mmp) cc_final: 0.6142 (ttt) REVERT: A 100 LEU cc_start: 0.8487 (mt) cc_final: 0.8118 (mp) REVERT: A 250 LEU cc_start: 0.9303 (tt) cc_final: 0.8930 (pp) REVERT: A 571 CYS cc_start: 0.9137 (t) cc_final: 0.8841 (t) REVERT: A 669 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7940 (mt-10) outliers start: 23 outliers final: 14 residues processed: 237 average time/residue: 0.1724 time to fit residues: 63.2334 Evaluate side-chains 203 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 619 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 123 optimal weight: 0.2980 chunk 130 optimal weight: 0.0770 chunk 64 optimal weight: 0.7980 chunk 116 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 492 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11211 Z= 0.195 Angle : 0.678 11.551 15240 Z= 0.344 Chirality : 0.045 0.302 1767 Planarity : 0.004 0.049 1864 Dihedral : 5.506 59.872 1469 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 2.54 % Allowed : 15.31 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.24), residues: 1351 helix: 0.91 (0.18), residues: 894 sheet: -3.21 (1.83), residues: 10 loop : -1.68 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 613 HIS 0.003 0.001 HIS A 447 PHE 0.043 0.002 PHE B 627 TYR 0.025 0.002 TYR A 171 ARG 0.002 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 201 time to evaluate : 1.255 Fit side-chains REVERT: B 3 PHE cc_start: 0.6391 (OUTLIER) cc_final: 0.6098 (m-80) REVERT: B 171 TYR cc_start: 0.9257 (OUTLIER) cc_final: 0.9009 (t80) REVERT: B 389 THR cc_start: 0.8733 (m) cc_final: 0.8513 (m) REVERT: B 489 MET cc_start: 0.8698 (ppp) cc_final: 0.8458 (ppp) REVERT: B 563 MET cc_start: 0.9100 (mmm) cc_final: 0.8466 (mmm) REVERT: B 594 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8993 (tt) REVERT: A 1 MET cc_start: 0.7159 (mmp) cc_final: 0.6373 (ttt) REVERT: A 21 MET cc_start: 0.9561 (mmm) cc_final: 0.9346 (mmm) REVERT: A 100 LEU cc_start: 0.8481 (mt) cc_final: 0.8153 (mp) REVERT: A 250 LEU cc_start: 0.9314 (tt) cc_final: 0.8946 (pp) REVERT: A 571 CYS cc_start: 0.9003 (t) cc_final: 0.8720 (t) REVERT: A 669 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7936 (mt-10) outliers start: 30 outliers final: 20 residues processed: 216 average time/residue: 0.1794 time to fit residues: 59.9186 Evaluate side-chains 216 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 193 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 PHE Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain A residue 80 ASP Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 653 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 30.0000 chunk 74 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 ASN B 492 ASN B 531 HIS B 628 GLN A 206 GLN A 447 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11211 Z= 0.273 Angle : 0.696 11.293 15240 Z= 0.357 Chirality : 0.045 0.252 1767 Planarity : 0.005 0.052 1864 Dihedral : 5.513 59.972 1469 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.13 % Allowed : 16.50 % Favored : 80.37 % 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 (0.24), residues: 1351 helix: 0.98 (0.18), residues: 887 sheet: -2.20 (1.29), residues: 20 loop : -1.78 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 613 HIS 0.003 0.001 HIS A 447 PHE 0.069 0.002 PHE B 627 TYR 0.027 0.002 TYR B 225 ARG 0.003 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 200 time to evaluate : 1.619 Fit side-chains revert: symmetry clash REVERT: B 49 TRP cc_start: 0.7784 (p90) cc_final: 0.7489 (p90) REVERT: B 171 TYR cc_start: 0.9288 (OUTLIER) cc_final: 0.9053 (t80) REVERT: B 198 ASP cc_start: 0.7908 (t0) cc_final: 0.7076 (t70) REVERT: B 357 PHE cc_start: 0.7457 (OUTLIER) cc_final: 0.6909 (m-10) REVERT: B 413 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9161 (mp) REVERT: B 414 GLU cc_start: 0.8889 (pt0) cc_final: 0.8353 (mt-10) REVERT: B 563 MET cc_start: 0.9189 (mmm) cc_final: 0.8482 (mmm) REVERT: A 250 LEU cc_start: 0.9301 (tt) cc_final: 0.9004 (pp) REVERT: A 440 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7642 (mt-10) REVERT: A 571 CYS cc_start: 0.9191 (t) cc_final: 0.8871 (t) REVERT: A 627 PHE cc_start: 0.6526 (m-80) cc_final: 0.6317 (m-80) REVERT: A 669 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8017 (mt-10) outliers start: 37 outliers final: 23 residues processed: 222 average time/residue: 0.1920 time to fit residues: 65.9208 Evaluate side-chains 214 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 188 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 653 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 25 optimal weight: 30.0000 chunk 76 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.8980 chunk 108 optimal weight: 30.0000 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 68 optimal weight: 30.0000 chunk 125 optimal weight: 0.7980 overall best weight: 0.8940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11211 Z= 0.213 Angle : 0.681 11.594 15240 Z= 0.345 Chirality : 0.044 0.257 1767 Planarity : 0.004 0.050 1864 Dihedral : 5.450 59.238 1469 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.13 % Allowed : 17.51 % Favored : 79.36 % 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: 0.14 (0.24), residues: 1351 helix: 1.09 (0.18), residues: 889 sheet: -2.15 (1.25), residues: 20 loop : -1.87 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 613 HIS 0.004 0.001 HIS A 447 PHE 0.067 0.002 PHE B 627 TYR 0.033 0.002 TYR A 377 ARG 0.002 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 200 time to evaluate : 1.214 Fit side-chains revert: symmetry clash REVERT: B 49 TRP cc_start: 0.7716 (p90) cc_final: 0.7417 (p90) REVERT: B 171 TYR cc_start: 0.9268 (OUTLIER) cc_final: 0.9020 (t80) REVERT: B 198 ASP cc_start: 0.7782 (t0) cc_final: 0.6948 (t70) REVERT: B 279 ASP cc_start: 0.8918 (OUTLIER) cc_final: 0.8690 (t0) REVERT: B 357 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6793 (m-10) REVERT: B 413 LEU cc_start: 0.9346 (OUTLIER) cc_final: 0.9136 (mp) REVERT: B 489 MET cc_start: 0.8668 (ppp) cc_final: 0.8155 (ppp) REVERT: B 563 MET cc_start: 0.9140 (mmm) cc_final: 0.8421 (mmm) REVERT: B 594 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8977 (tt) REVERT: A 21 MET cc_start: 0.9606 (mmm) cc_final: 0.9245 (mmm) REVERT: A 250 LEU cc_start: 0.9298 (tt) cc_final: 0.8999 (pp) REVERT: A 332 MET cc_start: 0.8289 (OUTLIER) cc_final: 0.7865 (mpp) REVERT: A 440 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 571 CYS cc_start: 0.9173 (t) cc_final: 0.8872 (t) REVERT: A 627 PHE cc_start: 0.6331 (m-80) cc_final: 0.6101 (m-80) REVERT: A 669 GLU cc_start: 0.8342 (mt-10) cc_final: 0.8000 (mt-10) outliers start: 37 outliers final: 21 residues processed: 221 average time/residue: 0.1714 time to fit residues: 58.7454 Evaluate side-chains 221 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 194 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 653 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 11211 Z= 0.353 Angle : 0.746 14.033 15240 Z= 0.379 Chirality : 0.046 0.249 1767 Planarity : 0.005 0.051 1864 Dihedral : 5.549 59.685 1469 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 3.64 % Allowed : 18.44 % Favored : 77.92 % 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 (0.24), residues: 1351 helix: 1.11 (0.18), residues: 875 sheet: -1.76 (1.14), residues: 27 loop : -1.82 (0.30), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 613 HIS 0.004 0.001 HIS A 447 PHE 0.077 0.002 PHE B 627 TYR 0.028 0.002 TYR B 225 ARG 0.003 0.000 ARG B 410 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 194 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.9182 (mpp) cc_final: 0.8760 (mpp) REVERT: B 49 TRP cc_start: 0.8001 (p90) cc_final: 0.7707 (p90) REVERT: B 56 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.7055 (mtp180) REVERT: B 171 TYR cc_start: 0.9313 (OUTLIER) cc_final: 0.9030 (t80) REVERT: B 198 ASP cc_start: 0.8000 (t0) cc_final: 0.7160 (t70) REVERT: B 357 PHE cc_start: 0.7456 (OUTLIER) cc_final: 0.6864 (m-10) REVERT: B 413 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9101 (mp) REVERT: B 563 MET cc_start: 0.9119 (mmm) cc_final: 0.8689 (mmm) REVERT: B 594 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9012 (tt) REVERT: A 21 MET cc_start: 0.9633 (mmm) cc_final: 0.9298 (mmm) REVERT: A 250 LEU cc_start: 0.9338 (tt) cc_final: 0.9038 (pp) REVERT: A 330 CYS cc_start: 0.8779 (t) cc_final: 0.8493 (t) REVERT: A 332 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8028 (mpp) REVERT: A 440 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7664 (mt-10) REVERT: A 571 CYS cc_start: 0.9274 (t) cc_final: 0.8955 (t) REVERT: A 669 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8018 (mt-10) outliers start: 43 outliers final: 26 residues processed: 218 average time/residue: 0.1924 time to fit residues: 64.7296 Evaluate side-chains 218 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 186 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 302 VAL Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 621 LEU Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 97 CYS Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 653 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 39 optimal weight: 0.0060 chunk 25 optimal weight: 30.0000 chunk 82 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 102 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11211 Z= 0.191 Angle : 0.705 12.806 15240 Z= 0.350 Chirality : 0.044 0.231 1767 Planarity : 0.004 0.050 1864 Dihedral : 5.425 58.020 1469 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.85 % Favored : 92.15 % Rotamer: Outliers : 3.05 % Allowed : 19.97 % Favored : 76.99 % 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: 0.32 (0.24), residues: 1351 helix: 1.27 (0.18), residues: 873 sheet: -2.11 (1.25), residues: 20 loop : -1.79 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 49 HIS 0.004 0.001 HIS A 447 PHE 0.061 0.002 PHE B 627 TYR 0.024 0.001 TYR B 171 ARG 0.003 0.000 ARG A 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 202 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.9274 (mpp) cc_final: 0.8929 (mpp) REVERT: B 49 TRP cc_start: 0.7780 (p90) cc_final: 0.7471 (p90) REVERT: B 56 ARG cc_start: 0.7134 (OUTLIER) cc_final: 0.6836 (mtp180) REVERT: B 171 TYR cc_start: 0.9253 (OUTLIER) cc_final: 0.9029 (t80) REVERT: B 198 ASP cc_start: 0.7778 (t0) cc_final: 0.6928 (t70) REVERT: B 279 ASP cc_start: 0.8881 (OUTLIER) cc_final: 0.8633 (t0) REVERT: B 332 MET cc_start: 0.7241 (mtp) cc_final: 0.6800 (mpp) REVERT: B 395 ARG cc_start: 0.8648 (ptm160) cc_final: 0.8401 (ptt180) REVERT: B 413 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9075 (mp) REVERT: B 563 MET cc_start: 0.9003 (mmm) cc_final: 0.8502 (mmm) REVERT: B 594 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8910 (tt) REVERT: B 691 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7840 (ptp-110) REVERT: A 21 MET cc_start: 0.9639 (mmm) cc_final: 0.9314 (mmm) REVERT: A 250 LEU cc_start: 0.9324 (tt) cc_final: 0.9027 (pp) REVERT: A 332 MET cc_start: 0.8241 (OUTLIER) cc_final: 0.7896 (mpp) REVERT: A 364 TYR cc_start: 0.7982 (m-80) cc_final: 0.7729 (m-80) REVERT: A 440 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7553 (mt-10) REVERT: A 571 CYS cc_start: 0.9086 (t) cc_final: 0.8774 (t) REVERT: A 652 THR cc_start: 0.8785 (m) cc_final: 0.8569 (m) REVERT: A 669 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7890 (mt-10) outliers start: 36 outliers final: 21 residues processed: 225 average time/residue: 0.1834 time to fit residues: 62.7547 Evaluate side-chains 218 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 190 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 171 TYR Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 566 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 619 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 0.4980 chunk 121 optimal weight: 0.0770 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 120 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 392 ASN ** A 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11211 Z= 0.233 Angle : 0.704 11.385 15240 Z= 0.353 Chirality : 0.045 0.228 1767 Planarity : 0.004 0.051 1864 Dihedral : 5.384 58.523 1469 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.14 % Favored : 91.86 % Rotamer: Outliers : 3.05 % Allowed : 20.30 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1351 helix: 1.26 (0.18), residues: 872 sheet: -2.03 (1.23), residues: 20 loop : -1.77 (0.30), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 613 HIS 0.003 0.001 HIS A 447 PHE 0.059 0.002 PHE B 627 TYR 0.031 0.002 TYR B 225 ARG 0.001 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 190 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1 MET cc_start: 0.9273 (mpp) cc_final: 0.8975 (mpp) REVERT: B 49 TRP cc_start: 0.7862 (p90) cc_final: 0.7551 (p90) REVERT: B 56 ARG cc_start: 0.7224 (OUTLIER) cc_final: 0.6928 (mtp180) REVERT: B 198 ASP cc_start: 0.7888 (t0) cc_final: 0.7017 (t70) REVERT: B 279 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8612 (t0) REVERT: B 332 MET cc_start: 0.7233 (mtp) cc_final: 0.6787 (mpp) REVERT: B 357 PHE cc_start: 0.7352 (OUTLIER) cc_final: 0.6723 (m-10) REVERT: B 413 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9067 (mp) REVERT: B 563 MET cc_start: 0.8998 (mmm) cc_final: 0.8526 (mmm) REVERT: B 594 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8949 (tt) REVERT: B 691 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7838 (ptp-110) REVERT: A 250 LEU cc_start: 0.9335 (tt) cc_final: 0.9032 (pp) REVERT: A 332 MET cc_start: 0.8307 (OUTLIER) cc_final: 0.7980 (mpp) REVERT: A 364 TYR cc_start: 0.8041 (m-80) cc_final: 0.7769 (m-80) REVERT: A 440 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7548 (mt-10) REVERT: A 571 CYS cc_start: 0.9105 (t) cc_final: 0.8802 (t) REVERT: A 669 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7938 (mt-10) outliers start: 36 outliers final: 23 residues processed: 214 average time/residue: 0.1477 time to fit residues: 48.7319 Evaluate side-chains 216 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 186 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 102 LEU Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 229 VAL Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 477 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 538 CYS Chi-restraints excluded: chain A residue 619 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 134 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11211 Z= 0.231 Angle : 0.723 15.162 15240 Z= 0.358 Chirality : 0.045 0.224 1767 Planarity : 0.004 0.050 1864 Dihedral : 5.353 58.448 1469 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 2.45 % Allowed : 21.07 % Favored : 76.48 % 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: 0.33 (0.24), residues: 1351 helix: 1.28 (0.18), residues: 866 sheet: -1.96 (1.23), residues: 20 loop : -1.76 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 613 HIS 0.005 0.001 HIS A 447 PHE 0.031 0.002 PHE B 513 TYR 0.030 0.002 TYR B 225 ARG 0.002 0.000 ARG B 410 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2702 Ramachandran restraints generated. 1351 Oldfield, 0 Emsley, 1351 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 183 time to evaluate : 1.224 Fit side-chains REVERT: B 1 MET cc_start: 0.9213 (mpp) cc_final: 0.8989 (mpp) REVERT: B 49 TRP cc_start: 0.7875 (p90) cc_final: 0.7568 (p90) REVERT: B 56 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6942 (mtp180) REVERT: B 198 ASP cc_start: 0.7872 (t0) cc_final: 0.7011 (t70) REVERT: B 279 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8614 (t0) REVERT: B 332 MET cc_start: 0.7224 (mtp) cc_final: 0.6797 (mpp) REVERT: B 357 PHE cc_start: 0.7334 (OUTLIER) cc_final: 0.6707 (m-10) REVERT: B 413 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9062 (mp) REVERT: B 563 MET cc_start: 0.9001 (mmm) cc_final: 0.8551 (mmm) REVERT: B 594 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8937 (tt) REVERT: B 691 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7833 (ptp-110) REVERT: A 250 LEU cc_start: 0.9363 (tt) cc_final: 0.9039 (pp) REVERT: A 332 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7960 (mpp) REVERT: A 364 TYR cc_start: 0.8018 (m-80) cc_final: 0.7752 (m-80) REVERT: A 440 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7534 (mt-10) REVERT: A 571 CYS cc_start: 0.9107 (t) cc_final: 0.8804 (t) REVERT: A 669 GLU cc_start: 0.8372 (mt-10) cc_final: 0.7948 (mt-10) outliers start: 29 outliers final: 18 residues processed: 201 average time/residue: 0.1770 time to fit residues: 54.8279 Evaluate side-chains 208 residues out of total 1182 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 183 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 56 ARG Chi-restraints excluded: chain B residue 190 GLU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 357 PHE Chi-restraints excluded: chain B residue 374 ILE Chi-restraints excluded: chain B residue 399 PHE Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 579 ILE Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 592 LEU Chi-restraints excluded: chain B residue 594 LEU Chi-restraints excluded: chain B residue 603 VAL Chi-restraints excluded: chain B residue 630 VAL Chi-restraints excluded: chain B residue 655 ILE Chi-restraints excluded: chain B residue 677 CYS Chi-restraints excluded: chain B residue 691 ARG Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 283 TYR Chi-restraints excluded: chain A residue 332 MET Chi-restraints excluded: chain A residue 374 ILE Chi-restraints excluded: chain A residue 381 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 513 PHE Chi-restraints excluded: chain A residue 619 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 15 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 110 optimal weight: 0.0570 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 0.1980 chunk 94 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 392 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.152229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110047 restraints weight = 20079.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.113714 restraints weight = 10273.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.116005 restraints weight = 7054.185| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11211 Z= 0.190 Angle : 0.717 14.812 15240 Z= 0.351 Chirality : 0.044 0.206 1767 Planarity : 0.004 0.049 1864 Dihedral : 5.263 58.175 1469 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.99 % Favored : 92.01 % Rotamer: Outliers : 2.71 % Allowed : 20.56 % Favored : 76.73 % 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: 0.38 (0.24), residues: 1351 helix: 1.31 (0.18), residues: 870 sheet: -2.00 (1.19), residues: 20 loop : -1.75 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 613 HIS 0.004 0.000 HIS A 447 PHE 0.032 0.001 PHE A 6 TYR 0.030 0.001 TYR B 225 ARG 0.002 0.000 ARG B 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2163.76 seconds wall clock time: 41 minutes 30.73 seconds (2490.73 seconds total)