Starting phenix.real_space_refine on Wed Feb 14 19:47:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/02_2024/8eob_28333_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/02_2024/8eob_28333.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/02_2024/8eob_28333.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/02_2024/8eob_28333.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/02_2024/8eob_28333_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8eob_28333/02_2024/8eob_28333_updated.pdb" } resolution = 3.1 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= 0.001 sd= 0.969 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 6411 2.51 5 N 1701 2.21 5 O 1975 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 430": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 520": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 304": "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: 10141 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 624, 5053 Classifications: {'peptide': 624} Link IDs: {'PTRANS': 17, 'TRANS': 606} Chain breaks: 2 Chain: "B" Number of atoms: 5024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 5024 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 17, 'TRANS': 603} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.84, per 1000 atoms: 0.58 Number of scatterers: 10141 At special positions: 0 Unit cell: (94.696, 94.696, 130.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 46 16.00 P 6 15.00 Mg 2 11.99 O 1975 8.00 N 1701 7.00 C 6411 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: 4.34 Conformation dependent library (CDL) restraints added in 1.9 seconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 9 sheets defined 40.2% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.20 Creating SS restraints... Processing helix chain 'A' and resid 21 through 31 Processing helix chain 'A' and resid 36 through 59 removed outlier: 3.716A pdb=" N PHE A 39 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LEU A 40 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE A 44 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS A 53 " --> pdb=" O ALA A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 Processing helix chain 'A' and resid 95 through 100 Processing helix chain 'A' and resid 109 through 116 Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 190 through 193 Processing helix chain 'A' and resid 195 through 204 Processing helix chain 'A' and resid 288 through 290 No H-bonds generated for 'chain 'A' and resid 288 through 290' Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 398 through 421 removed outlier: 4.035A pdb=" N GLU A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 443 removed outlier: 6.505A pdb=" N LYS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN A 436 " --> pdb=" O ALA A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 453 Processing helix chain 'A' and resid 469 through 475 Processing helix chain 'A' and resid 491 through 495 Processing helix chain 'A' and resid 501 through 506 removed outlier: 3.541A pdb=" N LYS A 505 " --> pdb=" O GLU A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 524 removed outlier: 3.552A pdb=" N GLN A 524 " --> pdb=" O CYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 561 through 570 Processing helix chain 'A' and resid 600 through 606 Processing helix chain 'A' and resid 614 through 619 removed outlier: 3.517A pdb=" N GLY A 618 " --> pdb=" O ASN A 614 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 619 " --> pdb=" O SER A 615 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 614 through 619' Processing helix chain 'A' and resid 633 through 644 Processing helix chain 'A' and resid 649 through 665 Processing helix chain 'A' and resid 673 through 688 Processing helix chain 'B' and resid 21 through 30 Processing helix chain 'B' and resid 36 through 59 removed outlier: 3.826A pdb=" N PHE B 39 " --> pdb=" O LYS B 36 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 40 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ILE B 44 " --> pdb=" O ARG B 41 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS B 53 " --> pdb=" O ALA B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 Processing helix chain 'B' and resid 95 through 100 Processing helix chain 'B' and resid 109 through 115 Processing helix chain 'B' and resid 133 through 138 Processing helix chain 'B' and resid 191 through 193 No H-bonds generated for 'chain 'B' and resid 191 through 193' Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 398 through 421 removed outlier: 4.148A pdb=" N GLU B 421 " --> pdb=" O SER B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 443 removed outlier: 6.411A pdb=" N LYS B 435 " --> pdb=" O GLU B 431 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ASN B 436 " --> pdb=" O ALA B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 454 removed outlier: 4.236A pdb=" N GLU B 453 " --> pdb=" O ARG B 449 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU B 454 " --> pdb=" O ARG B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 475 Processing helix chain 'B' and resid 491 through 495 Processing helix chain 'B' and resid 499 through 506 removed outlier: 4.030A pdb=" N ARG B 502 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 503 " --> pdb=" O VAL B 500 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ARG B 504 " --> pdb=" O GLU B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 524 removed outlier: 4.133A pdb=" N TYR B 520 " --> pdb=" O PRO B 516 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN B 524 " --> pdb=" O TYR B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 570 removed outlier: 5.482A pdb=" N ASN B 562 " --> pdb=" O ALA B 558 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N LEU B 563 " --> pdb=" O LYS B 559 " (cutoff:3.500A) Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 617 through 620 No H-bonds generated for 'chain 'B' and resid 617 through 620' Processing helix chain 'B' and resid 633 through 644 Processing helix chain 'B' and resid 649 through 666 Processing helix chain 'B' and resid 673 through 688 Processing sheet with id= A, first strand: chain 'A' and resid 212 through 216 removed outlier: 3.712A pdb=" N LYS A 142 " --> pdb=" O HIS A 184 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 217 through 219 Processing sheet with id= C, first strand: chain 'A' and resid 360 through 364 removed outlier: 6.879A pdb=" N LEU A 355 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ASP A 364 " --> pdb=" O ILE A 353 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE A 353 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N LYS A 354 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N GLY A 379 " --> pdb=" O LYS A 354 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N TYR A 356 " --> pdb=" O GLY A 379 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL A 381 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA A 317 " --> pdb=" O ILE A 335 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 532 through 535 Processing sheet with id= E, first strand: chain 'A' and resid 577 through 580 Processing sheet with id= F, first strand: chain 'B' and resid 165 through 169 removed outlier: 6.780A pdb=" N HIS B 184 " --> pdb=" O GLU B 141 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL B 143 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 182 " --> pdb=" O VAL B 143 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL B 145 " --> pdb=" O LYS B 180 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS B 180 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 147 " --> pdb=" O GLY B 178 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLY B 178 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N ILE B 75 " --> pdb=" O PRO B 212 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR B 214 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N TYR B 216 " --> pdb=" O PRO B 77 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 361 through 364 removed outlier: 7.048A pdb=" N LEU B 355 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N ASP B 364 " --> pdb=" O ILE B 353 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE B 353 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N LYS B 354 " --> pdb=" O ILE B 377 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY B 379 " --> pdb=" O LYS B 354 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N TYR B 356 " --> pdb=" O GLY B 379 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL B 381 " --> pdb=" O TYR B 356 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA B 317 " --> pdb=" O ILE B 335 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 532 through 535 Processing sheet with id= I, first strand: chain 'B' and resid 577 through 580 416 hydrogen bonds defined for protein. 1062 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: 3.09 Time building geometry restraints manager: 4.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3319 1.34 - 1.46: 2159 1.46 - 1.58: 4746 1.58 - 1.69: 5 1.69 - 1.81: 80 Bond restraints: 10309 Sorted by residual: bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.548 0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" O3A ANP B 801 " pdb=" PB ANP B 801 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 1.795 1.686 0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.690 0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.566 0.089 2.00e-02 2.50e+03 1.96e+01 ... (remaining 10304 not shown) Histogram of bond angle deviations from ideal: 98.87 - 105.90: 177 105.90 - 112.94: 5659 112.94 - 119.98: 3495 119.98 - 127.01: 4464 127.01 - 134.05: 82 Bond angle restraints: 13877 Sorted by residual: angle pdb=" PB ANP B 801 " pdb=" N3B ANP B 801 " pdb=" PG ANP B 801 " ideal model delta sigma weight residual 126.95 110.14 16.81 3.00e+00 1.11e-01 3.14e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 111.34 15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" O1B ANP A 801 " pdb=" PB ANP A 801 " pdb=" O2B ANP A 801 " ideal model delta sigma weight residual 120.08 109.21 10.87 3.00e+00 1.11e-01 1.31e+01 angle pdb=" O1B ANP B 801 " pdb=" PB ANP B 801 " pdb=" O2B ANP B 801 " ideal model delta sigma weight residual 120.08 109.37 10.71 3.00e+00 1.11e-01 1.27e+01 angle pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " pdb=" O2G ANP A 801 " ideal model delta sigma weight residual 101.05 110.02 -8.97 3.00e+00 1.11e-01 8.94e+00 ... (remaining 13872 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 5975 17.72 - 35.44: 343 35.44 - 53.15: 59 53.15 - 70.87: 8 70.87 - 88.59: 4 Dihedral angle restraints: 6389 sinusoidal: 2728 harmonic: 3661 Sorted by residual: dihedral pdb=" N LYS B 481 " pdb=" CA LYS B 481 " pdb=" CB LYS B 481 " pdb=" CG LYS B 481 " ideal model delta sinusoidal sigma weight residual -180.00 -125.36 -54.64 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" N ASN B 150 " pdb=" CA ASN B 150 " pdb=" CB ASN B 150 " pdb=" CG ASN B 150 " ideal model delta sinusoidal sigma weight residual -60.00 -113.44 53.44 3 1.50e+01 4.44e-03 9.20e+00 dihedral pdb=" CA GLU A 368 " pdb=" CB GLU A 368 " pdb=" CG GLU A 368 " pdb=" CD GLU A 368 " ideal model delta sinusoidal sigma weight residual 60.00 111.90 -51.90 3 1.50e+01 4.44e-03 9.06e+00 ... (remaining 6386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1288 0.052 - 0.104: 213 0.104 - 0.156: 42 0.156 - 0.208: 0 0.208 - 0.260: 2 Chirality restraints: 1545 Sorted by residual: chirality pdb=" C3' ANP A 801 " pdb=" C2' ANP A 801 " pdb=" C4' ANP A 801 " pdb=" O3' ANP A 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" C3' ANP B 801 " pdb=" C2' ANP B 801 " pdb=" C4' ANP B 801 " pdb=" O3' ANP B 801 " both_signs ideal model delta sigma weight residual False -2.36 -2.61 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE B 335 " pdb=" N ILE B 335 " pdb=" C ILE B 335 " pdb=" CB ILE B 335 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.16e-01 ... (remaining 1542 not shown) Planarity restraints: 1765 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 370 " 0.028 5.00e-02 4.00e+02 4.31e-02 2.97e+00 pdb=" N PRO A 371 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 370 " -0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO B 371 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 371 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 371 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 52 " -0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C ASP A 52 " 0.028 2.00e-02 2.50e+03 pdb=" O ASP A 52 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 53 " -0.009 2.00e-02 2.50e+03 ... (remaining 1762 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.54: 86 2.54 - 3.13: 7983 3.13 - 3.72: 15517 3.72 - 4.31: 21941 4.31 - 4.90: 37210 Nonbonded interactions: 82737 Sorted by model distance: nonbonded pdb=" O1B ANP B 801 " pdb=" O2G ANP B 801 " model vdw 1.945 3.040 nonbonded pdb=" O1B ANP B 801 " pdb="MG MG B 802 " model vdw 1.979 2.170 nonbonded pdb=" O2G ANP B 801 " pdb="MG MG B 802 " model vdw 1.988 2.170 nonbonded pdb=" N3B ANP A 801 " pdb="MG MG A 802 " model vdw 2.062 2.250 nonbonded pdb=" OD1 ASN B 46 " pdb="MG MG B 802 " model vdw 2.081 2.170 ... (remaining 82732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 220 or resid 275 through 345 or resid 351 throu \ gh 690 or resid 801 through 802)) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.400 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: 2.340 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 30.670 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.005 0.152 10309 Z= 0.294 Angle : 0.607 16.814 13877 Z= 0.296 Chirality : 0.041 0.260 1545 Planarity : 0.003 0.043 1765 Dihedral : 11.565 88.591 4015 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.78 % Allowed : 6.41 % Favored : 91.81 % 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: 0.42 (0.24), residues: 1233 helix: 1.34 (0.24), residues: 509 sheet: 0.36 (0.35), residues: 227 loop : -0.83 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 157 HIS 0.002 0.001 HIS B 458 PHE 0.009 0.001 PHE B 334 TYR 0.015 0.002 TYR A 134 ARG 0.002 0.000 ARG B 82 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 168 time to evaluate : 1.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 326 GLN cc_start: 0.8811 (pm20) cc_final: 0.8581 (pm20) REVERT: A 374 LEU cc_start: 0.9085 (OUTLIER) cc_final: 0.8840 (mp) REVERT: A 553 MET cc_start: 0.7275 (tpp) cc_final: 0.6984 (tpp) REVERT: A 606 MET cc_start: 0.8016 (ptp) cc_final: 0.7687 (ptp) REVERT: A 607 LYS cc_start: 0.8891 (ttpt) cc_final: 0.8389 (mttt) REVERT: A 629 ASN cc_start: 0.9296 (t0) cc_final: 0.8731 (t0) REVERT: A 636 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7378 (tm-30) REVERT: A 660 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8128 (mt-10) REVERT: B 70 GLU cc_start: 0.8044 (tt0) cc_final: 0.7730 (tt0) REVERT: B 118 GLN cc_start: 0.9042 (pp30) cc_final: 0.8560 (pp30) REVERT: B 196 ARG cc_start: 0.8440 (mmm-85) cc_final: 0.8206 (tpp80) REVERT: B 312 TRP cc_start: 0.8050 (p90) cc_final: 0.7792 (p90) REVERT: B 377 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8810 (mt) REVERT: B 490 SER cc_start: 0.8974 (t) cc_final: 0.8638 (t) REVERT: B 494 VAL cc_start: 0.9299 (t) cc_final: 0.8920 (m) REVERT: B 526 LYS cc_start: 0.9181 (mmtt) cc_final: 0.8912 (mmtm) REVERT: B 553 MET cc_start: 0.6635 (tpp) cc_final: 0.6204 (tpp) REVERT: B 581 SER cc_start: 0.8392 (t) cc_final: 0.7872 (t) REVERT: B 584 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8718 (mm) REVERT: B 599 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8430 (p) REVERT: B 602 MET cc_start: 0.8438 (tpp) cc_final: 0.7973 (tpp) REVERT: B 607 LYS cc_start: 0.8692 (tppt) cc_final: 0.8360 (mmtp) outliers start: 20 outliers final: 7 residues processed: 182 average time/residue: 0.2441 time to fit residues: 61.2147 Evaluate side-chains 123 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 584 LEU Chi-restraints excluded: chain B residue 599 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 50 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 37 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 7.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN A 676 HIS A 678 ASN B 80 GLN B 389 ASN B 493 GLN B 674 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 10309 Z= 0.248 Angle : 0.468 6.400 13877 Z= 0.246 Chirality : 0.040 0.149 1545 Planarity : 0.004 0.041 1765 Dihedral : 6.858 79.403 1430 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.58 % Allowed : 10.42 % Favored : 87.00 % 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: 0.58 (0.24), residues: 1233 helix: 1.41 (0.24), residues: 503 sheet: 0.49 (0.36), residues: 223 loop : -0.66 (0.27), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 157 HIS 0.002 0.001 HIS A 205 PHE 0.007 0.001 PHE A 165 TYR 0.013 0.001 TYR B 373 ARG 0.007 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 465 GLU cc_start: 0.8205 (pp20) cc_final: 0.7842 (pp20) REVERT: A 553 MET cc_start: 0.7289 (tpp) cc_final: 0.7021 (tpp) REVERT: A 602 MET cc_start: 0.8082 (tpp) cc_final: 0.7838 (tpp) REVERT: A 606 MET cc_start: 0.8109 (ptp) cc_final: 0.7855 (ptp) REVERT: A 607 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8392 (mttt) REVERT: A 619 TYR cc_start: 0.8500 (m-80) cc_final: 0.8082 (m-80) REVERT: A 621 MET cc_start: 0.8525 (mmm) cc_final: 0.7945 (mmm) REVERT: A 629 ASN cc_start: 0.9328 (t0) cc_final: 0.8828 (t0) REVERT: A 636 GLU cc_start: 0.7960 (mt-10) cc_final: 0.7380 (tm-30) REVERT: A 660 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8702 (mm-30) REVERT: B 70 GLU cc_start: 0.8010 (tt0) cc_final: 0.7721 (tt0) REVERT: B 114 MET cc_start: 0.8908 (tpp) cc_final: 0.8685 (mmm) REVERT: B 118 GLN cc_start: 0.9050 (pp30) cc_final: 0.8682 (pp30) REVERT: B 312 TRP cc_start: 0.8033 (p90) cc_final: 0.7797 (p90) REVERT: B 342 ASP cc_start: 0.6919 (OUTLIER) cc_final: 0.6326 (p0) REVERT: B 368 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6988 (pm20) REVERT: B 372 GLU cc_start: 0.8115 (tp30) cc_final: 0.7831 (tp30) REVERT: B 375 ASN cc_start: 0.8684 (p0) cc_final: 0.8411 (p0) REVERT: B 377 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8476 (mp) REVERT: B 490 SER cc_start: 0.8981 (t) cc_final: 0.8045 (p) REVERT: B 494 VAL cc_start: 0.9282 (t) cc_final: 0.8864 (m) REVERT: B 526 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8851 (mmtm) REVERT: B 545 GLU cc_start: 0.7599 (pm20) cc_final: 0.7313 (pm20) REVERT: B 546 ASP cc_start: 0.5750 (OUTLIER) cc_final: 0.5525 (p0) REVERT: B 553 MET cc_start: 0.6902 (tpp) cc_final: 0.6408 (tpp) REVERT: B 581 SER cc_start: 0.8387 (t) cc_final: 0.7943 (t) REVERT: B 599 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8381 (p) REVERT: B 602 MET cc_start: 0.8464 (tpp) cc_final: 0.8007 (tpp) REVERT: B 607 LYS cc_start: 0.8523 (tppt) cc_final: 0.8285 (mttm) REVERT: B 629 ASN cc_start: 0.9108 (t0) cc_final: 0.8875 (t0) outliers start: 29 outliers final: 15 residues processed: 136 average time/residue: 0.2223 time to fit residues: 43.4169 Evaluate side-chains 125 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 105 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 486 ILE Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 599 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 8.9990 chunk 121 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 389 ASN A 678 ASN B 674 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10309 Z= 0.168 Angle : 0.431 5.195 13877 Z= 0.227 Chirality : 0.039 0.140 1545 Planarity : 0.003 0.040 1765 Dihedral : 6.053 75.607 1426 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.40 % Allowed : 11.49 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1233 helix: 1.56 (0.24), residues: 492 sheet: 0.60 (0.36), residues: 223 loop : -0.57 (0.27), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 157 HIS 0.001 0.000 HIS B 632 PHE 0.006 0.001 PHE A 165 TYR 0.012 0.001 TYR B 373 ARG 0.004 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LYS cc_start: 0.8114 (mttm) cc_final: 0.7897 (mtmt) REVERT: A 465 GLU cc_start: 0.8130 (pp20) cc_final: 0.7745 (pp20) REVERT: A 553 MET cc_start: 0.7229 (tpp) cc_final: 0.6924 (tpp) REVERT: A 602 MET cc_start: 0.7947 (tpp) cc_final: 0.7684 (tpp) REVERT: A 606 MET cc_start: 0.8030 (OUTLIER) cc_final: 0.7781 (ptp) REVERT: A 607 LYS cc_start: 0.8905 (ttpt) cc_final: 0.8407 (mttt) REVERT: A 629 ASN cc_start: 0.9335 (t0) cc_final: 0.8814 (t0) REVERT: A 636 GLU cc_start: 0.7943 (mt-10) cc_final: 0.7696 (tm-30) REVERT: A 660 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8726 (mm-30) REVERT: B 70 GLU cc_start: 0.7949 (tt0) cc_final: 0.7692 (tt0) REVERT: B 118 GLN cc_start: 0.9029 (pp30) cc_final: 0.8661 (pp30) REVERT: B 312 TRP cc_start: 0.8008 (p90) cc_final: 0.7794 (p90) REVERT: B 368 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: B 372 GLU cc_start: 0.8120 (tp30) cc_final: 0.7830 (tp30) REVERT: B 375 ASN cc_start: 0.8677 (p0) cc_final: 0.8388 (p0) REVERT: B 490 SER cc_start: 0.8982 (t) cc_final: 0.8065 (p) REVERT: B 494 VAL cc_start: 0.9261 (t) cc_final: 0.8868 (m) REVERT: B 526 LYS cc_start: 0.9174 (mmtt) cc_final: 0.8885 (mmtm) REVERT: B 553 MET cc_start: 0.6762 (tpp) cc_final: 0.6284 (tpp) REVERT: B 599 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8278 (p) REVERT: B 602 MET cc_start: 0.8446 (tpp) cc_final: 0.7893 (tpp) REVERT: B 607 LYS cc_start: 0.8497 (tppt) cc_final: 0.8260 (mttm) REVERT: B 617 MET cc_start: 0.6827 (mmt) cc_final: 0.6468 (mmt) REVERT: B 629 ASN cc_start: 0.8998 (t0) cc_final: 0.8761 (t0) outliers start: 27 outliers final: 12 residues processed: 137 average time/residue: 0.2103 time to fit residues: 41.9094 Evaluate side-chains 119 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 0.0470 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 overall best weight: 1.3682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 523 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10309 Z= 0.180 Angle : 0.423 4.970 13877 Z= 0.224 Chirality : 0.039 0.139 1545 Planarity : 0.003 0.041 1765 Dihedral : 5.610 72.038 1417 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.58 % Allowed : 11.75 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.25), residues: 1233 helix: 1.60 (0.24), residues: 490 sheet: 0.57 (0.36), residues: 225 loop : -0.56 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 157 HIS 0.002 0.000 HIS B 632 PHE 0.007 0.001 PHE B 334 TYR 0.012 0.001 TYR B 373 ARG 0.002 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 106 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.9319 (tpp) cc_final: 0.8953 (tpp) REVERT: A 406 LYS cc_start: 0.8107 (mttm) cc_final: 0.7900 (mtmt) REVERT: A 465 GLU cc_start: 0.8092 (pp20) cc_final: 0.7699 (pp20) REVERT: A 553 MET cc_start: 0.7334 (tpp) cc_final: 0.7061 (tpp) REVERT: A 572 ASP cc_start: 0.8282 (t0) cc_final: 0.8029 (m-30) REVERT: A 606 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7710 (ptp) REVERT: A 607 LYS cc_start: 0.8908 (ttpt) cc_final: 0.8405 (mttt) REVERT: A 629 ASN cc_start: 0.9341 (t0) cc_final: 0.9004 (t0) REVERT: A 636 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7711 (tm-30) REVERT: A 660 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8703 (mm-30) REVERT: B 70 GLU cc_start: 0.7954 (tt0) cc_final: 0.7707 (tt0) REVERT: B 118 GLN cc_start: 0.9054 (pp30) cc_final: 0.8667 (pp30) REVERT: B 312 TRP cc_start: 0.7965 (p90) cc_final: 0.7765 (p90) REVERT: B 342 ASP cc_start: 0.6918 (OUTLIER) cc_final: 0.6367 (p0) REVERT: B 368 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7039 (pm20) REVERT: B 372 GLU cc_start: 0.8080 (tp30) cc_final: 0.7767 (tp30) REVERT: B 375 ASN cc_start: 0.8671 (p0) cc_final: 0.8435 (p0) REVERT: B 490 SER cc_start: 0.8991 (t) cc_final: 0.8186 (p) REVERT: B 515 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7980 (mm-30) REVERT: B 526 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8840 (mmtm) REVERT: B 553 MET cc_start: 0.6900 (tpp) cc_final: 0.6442 (tpp) REVERT: B 607 LYS cc_start: 0.8485 (tppt) cc_final: 0.8238 (mttm) REVERT: B 629 ASN cc_start: 0.9042 (t0) cc_final: 0.8790 (t0) outliers start: 29 outliers final: 18 residues processed: 130 average time/residue: 0.2137 time to fit residues: 40.2936 Evaluate side-chains 129 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 107 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 552 LYS Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 678 ASN Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.0060 chunk 68 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10309 Z= 0.187 Angle : 0.422 5.668 13877 Z= 0.224 Chirality : 0.039 0.142 1545 Planarity : 0.003 0.040 1765 Dihedral : 5.425 68.176 1414 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.49 % Allowed : 11.93 % Favored : 85.57 % 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: 0.78 (0.25), residues: 1233 helix: 1.62 (0.24), residues: 490 sheet: 0.61 (0.36), residues: 225 loop : -0.56 (0.28), residues: 518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 157 HIS 0.002 0.000 HIS B 632 PHE 0.007 0.001 PHE B 334 TYR 0.012 0.001 TYR B 373 ARG 0.002 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.9309 (tpp) cc_final: 0.8951 (tpp) REVERT: A 374 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8693 (mp) REVERT: A 406 LYS cc_start: 0.8145 (mttm) cc_final: 0.7941 (mtmt) REVERT: A 465 GLU cc_start: 0.8064 (pp20) cc_final: 0.7665 (pp20) REVERT: A 553 MET cc_start: 0.7323 (tpp) cc_final: 0.7041 (tpp) REVERT: A 606 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.7954 (ptp) REVERT: A 607 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8397 (mttt) REVERT: A 629 ASN cc_start: 0.9337 (t0) cc_final: 0.9008 (t0) REVERT: A 636 GLU cc_start: 0.8031 (mt-10) cc_final: 0.7438 (tm-30) REVERT: A 660 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8468 (mm-30) REVERT: B 70 GLU cc_start: 0.7967 (tt0) cc_final: 0.7724 (tt0) REVERT: B 118 GLN cc_start: 0.9041 (pp30) cc_final: 0.8646 (pp30) REVERT: B 342 ASP cc_start: 0.6807 (OUTLIER) cc_final: 0.6260 (p0) REVERT: B 368 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7015 (pm20) REVERT: B 372 GLU cc_start: 0.8099 (tp30) cc_final: 0.7784 (tp30) REVERT: B 375 ASN cc_start: 0.8672 (p0) cc_final: 0.8440 (p0) REVERT: B 490 SER cc_start: 0.8993 (t) cc_final: 0.8188 (p) REVERT: B 526 LYS cc_start: 0.9141 (mmtt) cc_final: 0.8821 (mmtm) REVERT: B 553 MET cc_start: 0.6913 (tpp) cc_final: 0.6438 (tpp) REVERT: B 564 CYS cc_start: 0.8768 (m) cc_final: 0.8427 (m) REVERT: B 607 LYS cc_start: 0.8537 (tppt) cc_final: 0.8290 (mttm) REVERT: B 617 MET cc_start: 0.6948 (mmt) cc_final: 0.6306 (mmt) REVERT: B 629 ASN cc_start: 0.8987 (t0) cc_final: 0.8742 (t0) outliers start: 28 outliers final: 21 residues processed: 128 average time/residue: 0.2238 time to fit residues: 41.3839 Evaluate side-chains 128 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 654 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 537 THR Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 0.0670 chunk 23 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 99 optimal weight: 0.3980 chunk 55 optimal weight: 0.0070 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10309 Z= 0.107 Angle : 0.391 5.661 13877 Z= 0.209 Chirality : 0.038 0.135 1545 Planarity : 0.003 0.039 1765 Dihedral : 5.055 61.204 1414 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.78 % Allowed : 13.18 % Favored : 85.04 % 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: 0.76 (0.25), residues: 1233 helix: 1.47 (0.24), residues: 518 sheet: 0.68 (0.36), residues: 231 loop : -0.58 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 157 HIS 0.001 0.000 HIS A 632 PHE 0.006 0.001 PHE B 334 TYR 0.010 0.001 TYR B 373 ARG 0.002 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 121 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7968 (tt) REVERT: A 406 LYS cc_start: 0.8207 (mttm) cc_final: 0.7967 (mtmt) REVERT: A 465 GLU cc_start: 0.7969 (pp20) cc_final: 0.7542 (pp20) REVERT: A 553 MET cc_start: 0.7346 (tpp) cc_final: 0.7041 (tpp) REVERT: A 606 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.7976 (ptp) REVERT: A 607 LYS cc_start: 0.8829 (ttpt) cc_final: 0.8388 (mttt) REVERT: A 629 ASN cc_start: 0.9311 (t0) cc_final: 0.9027 (t0) REVERT: A 636 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7430 (tm-30) REVERT: A 660 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8167 (mt-10) REVERT: B 118 GLN cc_start: 0.9010 (pp30) cc_final: 0.8705 (pp30) REVERT: B 333 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8630 (mt) REVERT: B 342 ASP cc_start: 0.6718 (OUTLIER) cc_final: 0.5993 (p0) REVERT: B 368 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6799 (pm20) REVERT: B 372 GLU cc_start: 0.7968 (tp30) cc_final: 0.7577 (tp30) REVERT: B 375 ASN cc_start: 0.8634 (p0) cc_final: 0.8409 (p0) REVERT: B 490 SER cc_start: 0.8995 (t) cc_final: 0.8186 (p) REVERT: B 492 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8311 (mm-30) REVERT: B 515 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.8014 (mm-30) REVERT: B 526 LYS cc_start: 0.9130 (mmtt) cc_final: 0.8776 (mmtm) REVERT: B 553 MET cc_start: 0.6893 (tpp) cc_final: 0.6458 (tpp) outliers start: 20 outliers final: 12 residues processed: 134 average time/residue: 0.2246 time to fit residues: 43.3450 Evaluate side-chains 127 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 631 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 66 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.0770 chunk 55 optimal weight: 10.0000 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN B 523 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 10309 Z= 0.191 Angle : 0.432 6.647 13877 Z= 0.227 Chirality : 0.039 0.138 1545 Planarity : 0.003 0.042 1765 Dihedral : 5.161 63.048 1412 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.23 % Allowed : 13.89 % Favored : 83.88 % 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: 0.87 (0.25), residues: 1233 helix: 1.66 (0.24), residues: 490 sheet: 0.72 (0.36), residues: 231 loop : -0.52 (0.28), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 157 HIS 0.002 0.000 HIS B 632 PHE 0.007 0.001 PHE B 334 TYR 0.011 0.001 TYR B 134 ARG 0.001 0.000 ARG B 612 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 103 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.9320 (tpp) cc_final: 0.8972 (tpp) REVERT: A 343 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7990 (tt) REVERT: A 406 LYS cc_start: 0.8213 (mttm) cc_final: 0.7982 (mtmt) REVERT: A 465 GLU cc_start: 0.8012 (pp20) cc_final: 0.7578 (pp20) REVERT: A 553 MET cc_start: 0.7311 (tpp) cc_final: 0.7023 (tpp) REVERT: A 567 MET cc_start: 0.8530 (mtm) cc_final: 0.8154 (mtt) REVERT: A 606 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.8032 (ptp) REVERT: A 607 LYS cc_start: 0.8785 (ttpt) cc_final: 0.8386 (mttt) REVERT: A 629 ASN cc_start: 0.9340 (t0) cc_final: 0.9048 (t0) REVERT: A 636 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7451 (tm-30) REVERT: A 660 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8143 (mt-10) REVERT: B 118 GLN cc_start: 0.9021 (pp30) cc_final: 0.8711 (pp30) REVERT: B 333 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8664 (mt) REVERT: B 342 ASP cc_start: 0.6795 (OUTLIER) cc_final: 0.6093 (p0) REVERT: B 368 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.6781 (pm20) REVERT: B 372 GLU cc_start: 0.7989 (tp30) cc_final: 0.7592 (tp30) REVERT: B 375 ASN cc_start: 0.8653 (p0) cc_final: 0.8428 (p0) REVERT: B 490 SER cc_start: 0.9012 (t) cc_final: 0.8220 (p) REVERT: B 515 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7957 (mm-30) REVERT: B 553 MET cc_start: 0.6893 (tpp) cc_final: 0.6441 (tpp) outliers start: 25 outliers final: 17 residues processed: 120 average time/residue: 0.2171 time to fit residues: 37.9422 Evaluate side-chains 125 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 102 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 536 VAL Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.0000 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 59 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10309 Z= 0.173 Angle : 0.435 7.121 13877 Z= 0.226 Chirality : 0.039 0.140 1545 Planarity : 0.003 0.041 1765 Dihedral : 5.203 64.073 1412 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.32 % Allowed : 13.45 % Favored : 84.24 % 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: 0.80 (0.25), residues: 1233 helix: 1.52 (0.24), residues: 500 sheet: 0.82 (0.35), residues: 229 loop : -0.57 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 157 HIS 0.002 0.000 HIS B 632 PHE 0.006 0.001 PHE B 334 TYR 0.011 0.001 TYR B 134 ARG 0.001 0.000 ARG A 450 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 103 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7938 (tt) REVERT: A 406 LYS cc_start: 0.8200 (mttm) cc_final: 0.7978 (mtmt) REVERT: A 465 GLU cc_start: 0.8072 (pp20) cc_final: 0.7658 (pp20) REVERT: A 553 MET cc_start: 0.7369 (tpp) cc_final: 0.7081 (tpp) REVERT: A 606 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.7992 (ptp) REVERT: A 607 LYS cc_start: 0.8725 (ttpt) cc_final: 0.8316 (mttt) REVERT: A 629 ASN cc_start: 0.9336 (t0) cc_final: 0.9069 (t0) REVERT: A 636 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7408 (tm-30) REVERT: A 660 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8115 (mt-10) REVERT: B 70 GLU cc_start: 0.8212 (tt0) cc_final: 0.7939 (pt0) REVERT: B 118 GLN cc_start: 0.9014 (pp30) cc_final: 0.8711 (pp30) REVERT: B 333 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8630 (mt) REVERT: B 342 ASP cc_start: 0.6786 (OUTLIER) cc_final: 0.6096 (p0) REVERT: B 366 CYS cc_start: 0.8050 (t) cc_final: 0.7571 (m) REVERT: B 368 GLU cc_start: 0.7154 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: B 372 GLU cc_start: 0.8010 (tp30) cc_final: 0.7579 (tp30) REVERT: B 375 ASN cc_start: 0.8660 (p0) cc_final: 0.8435 (p0) REVERT: B 490 SER cc_start: 0.9034 (t) cc_final: 0.8247 (p) REVERT: B 515 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7941 (mm-30) REVERT: B 553 MET cc_start: 0.6880 (tpp) cc_final: 0.6422 (tpp) outliers start: 26 outliers final: 17 residues processed: 121 average time/residue: 0.2200 time to fit residues: 38.5102 Evaluate side-chains 128 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 105 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 546 ASP Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 7.9990 chunk 104 optimal weight: 7.9990 chunk 111 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 20.0000 chunk 87 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 100 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 10309 Z= 0.236 Angle : 0.472 6.697 13877 Z= 0.243 Chirality : 0.040 0.138 1545 Planarity : 0.003 0.041 1765 Dihedral : 5.372 66.647 1412 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.40 % Allowed : 13.71 % Favored : 83.88 % 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: 0.80 (0.25), residues: 1233 helix: 1.57 (0.24), residues: 496 sheet: 0.74 (0.35), residues: 230 loop : -0.59 (0.28), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 157 HIS 0.003 0.001 HIS B 632 PHE 0.007 0.001 PHE B 334 TYR 0.014 0.001 TYR A 211 ARG 0.002 0.000 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 100 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.7983 (tt) REVERT: A 374 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8603 (mp) REVERT: A 406 LYS cc_start: 0.8215 (mttm) cc_final: 0.7994 (mtmt) REVERT: A 465 GLU cc_start: 0.8099 (pp20) cc_final: 0.7661 (pp20) REVERT: A 553 MET cc_start: 0.7360 (tpp) cc_final: 0.7071 (tpp) REVERT: A 606 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8031 (ptp) REVERT: A 607 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8270 (mttt) REVERT: A 629 ASN cc_start: 0.9348 (t0) cc_final: 0.9060 (t0) REVERT: A 636 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7406 (tm-30) REVERT: A 660 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8154 (mt-10) REVERT: B 70 GLU cc_start: 0.8213 (tt0) cc_final: 0.7880 (pt0) REVERT: B 118 GLN cc_start: 0.9030 (pp30) cc_final: 0.8744 (pp30) REVERT: B 342 ASP cc_start: 0.6799 (OUTLIER) cc_final: 0.6084 (p0) REVERT: B 366 CYS cc_start: 0.8060 (t) cc_final: 0.7616 (m) REVERT: B 368 GLU cc_start: 0.7226 (OUTLIER) cc_final: 0.6751 (pm20) REVERT: B 372 GLU cc_start: 0.8053 (tp30) cc_final: 0.7694 (tp30) REVERT: B 375 ASN cc_start: 0.8661 (p0) cc_final: 0.8368 (p0) REVERT: B 490 SER cc_start: 0.8991 (t) cc_final: 0.8197 (p) REVERT: B 515 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7909 (mm-30) REVERT: B 553 MET cc_start: 0.6873 (tpp) cc_final: 0.6406 (tpp) outliers start: 27 outliers final: 19 residues processed: 119 average time/residue: 0.2570 time to fit residues: 47.4114 Evaluate side-chains 123 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 98 time to evaluate : 3.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 chunk 10 optimal weight: 0.0000 chunk 75 optimal weight: 5.9990 chunk 60 optimal weight: 0.0270 chunk 78 optimal weight: 3.9990 overall best weight: 1.5846 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10309 Z= 0.197 Angle : 0.454 6.584 13877 Z= 0.236 Chirality : 0.039 0.141 1545 Planarity : 0.003 0.040 1765 Dihedral : 5.328 66.601 1412 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.23 % Allowed : 13.80 % Favored : 83.97 % 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: 0.74 (0.25), residues: 1233 helix: 1.43 (0.24), residues: 507 sheet: 0.74 (0.35), residues: 230 loop : -0.57 (0.28), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 157 HIS 0.002 0.000 HIS B 632 PHE 0.007 0.001 PHE B 334 TYR 0.012 0.001 TYR B 134 ARG 0.002 0.000 ARG A 450 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 102 time to evaluate : 1.325 Fit side-chains revert: symmetry clash REVERT: A 61 ASP cc_start: 0.7945 (t0) cc_final: 0.7727 (t0) REVERT: A 93 MET cc_start: 0.9120 (mtm) cc_final: 0.8904 (mtp) REVERT: A 343 LEU cc_start: 0.8294 (OUTLIER) cc_final: 0.7983 (tt) REVERT: A 406 LYS cc_start: 0.8205 (mttm) cc_final: 0.7985 (mtmt) REVERT: A 465 GLU cc_start: 0.8095 (pp20) cc_final: 0.7673 (pp20) REVERT: A 553 MET cc_start: 0.7473 (tpp) cc_final: 0.7197 (tpp) REVERT: A 606 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.7864 (ptp) REVERT: A 607 LYS cc_start: 0.8654 (ttpt) cc_final: 0.8257 (mttt) REVERT: A 629 ASN cc_start: 0.9341 (t0) cc_final: 0.9068 (t0) REVERT: A 636 GLU cc_start: 0.8014 (mt-10) cc_final: 0.7434 (tm-30) REVERT: A 660 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8517 (mm-30) REVERT: B 70 GLU cc_start: 0.8183 (tt0) cc_final: 0.7840 (pt0) REVERT: B 118 GLN cc_start: 0.9027 (pp30) cc_final: 0.8742 (pp30) REVERT: B 333 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8682 (mt) REVERT: B 342 ASP cc_start: 0.6777 (OUTLIER) cc_final: 0.6077 (p0) REVERT: B 366 CYS cc_start: 0.8050 (t) cc_final: 0.7576 (m) REVERT: B 368 GLU cc_start: 0.7227 (OUTLIER) cc_final: 0.6775 (pm20) REVERT: B 372 GLU cc_start: 0.8059 (tp30) cc_final: 0.7691 (tp30) REVERT: B 375 ASN cc_start: 0.8664 (p0) cc_final: 0.8434 (p0) REVERT: B 490 SER cc_start: 0.8982 (t) cc_final: 0.8183 (p) REVERT: B 515 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7947 (mm-30) REVERT: B 553 MET cc_start: 0.6896 (tpp) cc_final: 0.6428 (tpp) REVERT: B 602 MET cc_start: 0.8411 (tpt) cc_final: 0.7943 (tpp) outliers start: 25 outliers final: 19 residues processed: 120 average time/residue: 0.2196 time to fit residues: 38.3784 Evaluate side-chains 126 residues out of total 1123 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 101 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain A residue 514 THR Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 677 SER Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 86 LEU Chi-restraints excluded: chain B residue 125 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 342 ASP Chi-restraints excluded: chain B residue 368 GLU Chi-restraints excluded: chain B residue 370 ILE Chi-restraints excluded: chain B residue 441 ILE Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain B residue 479 THR Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain B residue 514 THR Chi-restraints excluded: chain B residue 515 GLU Chi-restraints excluded: chain B residue 546 ASP Chi-restraints excluded: chain B residue 575 VAL Chi-restraints excluded: chain B residue 590 CYS Chi-restraints excluded: chain B residue 593 THR Chi-restraints excluded: chain B residue 631 ASP Chi-restraints excluded: chain B residue 670 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 30 optimal weight: 3.9990 chunk 90 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 86 optimal weight: 0.3980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.101321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.079956 restraints weight = 18107.386| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.80 r_work: 0.2861 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10309 Z= 0.131 Angle : 0.439 8.069 13877 Z= 0.227 Chirality : 0.038 0.137 1545 Planarity : 0.003 0.041 1765 Dihedral : 5.156 65.511 1412 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.05 % Allowed : 14.07 % Favored : 83.88 % 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: 0.80 (0.25), residues: 1233 helix: 1.46 (0.24), residues: 507 sheet: 0.85 (0.35), residues: 229 loop : -0.55 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 157 HIS 0.001 0.000 HIS B 632 PHE 0.006 0.001 PHE B 334 TYR 0.011 0.001 TYR A 134 ARG 0.002 0.000 ARG A 450 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2125.20 seconds wall clock time: 39 minutes 48.94 seconds (2388.94 seconds total)