Starting phenix.real_space_refine on Fri Mar 15 01:54:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou0_13071/03_2024/7ou0_13071_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou0_13071/03_2024/7ou0_13071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou0_13071/03_2024/7ou0_13071.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou0_13071/03_2024/7ou0_13071.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou0_13071/03_2024/7ou0_13071_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ou0_13071/03_2024/7ou0_13071_updated.pdb" } resolution = 3.8 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 ------------------------------------------------------------------------------- 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= 0.002 sd= 0.009 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: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6472 2.51 5 N 1839 2.21 5 O 1965 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 186": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 220": "NH1" <-> "NH2" Residue "B ARG 249": "NH1" <-> "NH2" Residue "B GLU 261": "OE1" <-> "OE2" Residue "B GLU 263": "OE1" <-> "OE2" Residue "B GLU 288": "OE1" <-> "OE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B ARG 369": "NH1" <-> "NH2" Residue "B GLU 402": "OE1" <-> "OE2" Residue "B ARG 656": "NH1" <-> "NH2" Residue "B GLU 676": "OE1" <-> "OE2" Residue "B GLU 686": "OE1" <-> "OE2" Residue "B GLU 694": "OE1" <-> "OE2" Residue "B ARG 697": "NH1" <-> "NH2" Residue "B GLU 751": "OE1" <-> "OE2" Residue "B GLU 795": "OE1" <-> "OE2" Residue "A GLU 88": "OE1" <-> "OE2" Residue "A ARG 108": "NH1" <-> "NH2" Residue "A GLU 122": "OE1" <-> "OE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A ARG 156": "NH1" <-> "NH2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A ARG 193": "NH1" <-> "NH2" Residue "A GLU 263": "OE1" <-> "OE2" Residue "A ARG 369": "NH1" <-> "NH2" Residue "A GLU 530": "OE1" <-> "OE2" Residue "A GLU 540": "OE1" <-> "OE2" Residue "A GLU 646": "OE1" <-> "OE2" Residue "A GLU 694": "OE1" <-> "OE2" Residue "A ARG 697": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10335 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 602, 4697 Classifications: {'peptide': 602} Link IDs: {'PTRANS': 25, 'TRANS': 576} Chain breaks: 1 Chain: "A" Number of atoms: 5572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 711, 5572 Classifications: {'peptide': 711} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 679} Chain breaks: 3 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 38 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.82, per 1000 atoms: 0.56 Number of scatterers: 10335 At special positions: 0 Unit cell: (113.52, 121.44, 97.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 2 22.97 S 51 16.00 P 4 15.00 Mg 2 11.99 O 1965 8.00 N 1839 7.00 C 6472 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: 4.28 Conformation dependent library (CDL) restraints added in 2.0 seconds 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2458 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 9 sheets defined 48.6% alpha, 10.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.32 Creating SS restraints... Processing helix chain 'B' and resid 163 through 173 Processing helix chain 'B' and resid 187 through 190 Processing helix chain 'B' and resid 201 through 204 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 231 through 247 Processing helix chain 'B' and resid 252 through 254 No H-bonds generated for 'chain 'B' and resid 252 through 254' Processing helix chain 'B' and resid 271 through 277 Processing helix chain 'B' and resid 291 through 295 Processing helix chain 'B' and resid 301 through 312 Processing helix chain 'B' and resid 318 through 330 Processing helix chain 'B' and resid 335 through 345 Proline residue: B 340 - end of helix Processing helix chain 'B' and resid 349 through 356 Processing helix chain 'B' and resid 362 through 384 Proline residue: B 376 - end of helix removed outlier: 3.777A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 397 Processing helix chain 'B' and resid 401 through 410 Processing helix chain 'B' and resid 431 through 440 Processing helix chain 'B' and resid 512 through 565 Proline residue: B 537 - end of helix removed outlier: 4.735A pdb=" N GLU B 540 " --> pdb=" O LEU B 536 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N ALA B 541 " --> pdb=" O PRO B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 591 removed outlier: 4.056A pdb=" N GLN B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 636 Processing helix chain 'B' and resid 669 through 683 Processing helix chain 'B' and resid 701 through 717 Processing helix chain 'B' and resid 732 through 738 Proline residue: B 736 - end of helix Processing helix chain 'B' and resid 772 through 779 Processing helix chain 'B' and resid 783 through 798 Processing helix chain 'A' and resid 12 through 23 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 73 through 86 removed outlier: 4.946A pdb=" N GLU A 77 " --> pdb=" O HIS A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 173 Processing helix chain 'A' and resid 201 through 204 Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 231 through 248 Processing helix chain 'A' and resid 271 through 276 Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 301 through 312 Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 335 through 345 Proline residue: A 340 - end of helix removed outlier: 3.518A pdb=" N GLN A 344 " --> pdb=" O PRO A 340 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 362 through 384 Proline residue: A 376 - end of helix removed outlier: 3.509A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 397 Processing helix chain 'A' and resid 401 through 410 Processing helix chain 'A' and resid 419 through 421 No H-bonds generated for 'chain 'A' and resid 419 through 421' Processing helix chain 'A' and resid 431 through 441 Processing helix chain 'A' and resid 513 through 565 Proline residue: A 537 - end of helix removed outlier: 4.915A pdb=" N GLU A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N ALA A 541 " --> pdb=" O PRO A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 591 removed outlier: 3.788A pdb=" N GLN A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 636 removed outlier: 3.568A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 683 Processing helix chain 'A' and resid 701 through 717 Processing helix chain 'A' and resid 730 through 738 Proline residue: A 736 - end of helix Processing helix chain 'A' and resid 772 through 779 Processing helix chain 'A' and resid 783 through 799 Processing sheet with id= A, first strand: chain 'B' and resid 196 through 199 removed outlier: 5.900A pdb=" N LEU B 178 " --> pdb=" O ARG B 197 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ARG B 199 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TYR B 180 " --> pdb=" O ARG B 199 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 181 " --> pdb=" O ILE B 136 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N GLN B 138 " --> pdb=" O ALA B 181 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG B 154 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 570 through 572 removed outlier: 6.666A pdb=" N VAL B 645 " --> pdb=" O THR B 571 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 762 through 764 removed outlier: 6.467A pdb=" N MET B 609 " --> pdb=" O ALA B 743 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL B 745 " --> pdb=" O MET B 609 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N ILE B 611 " --> pdb=" O VAL B 745 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU B 747 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B 613 " --> pdb=" O LEU B 747 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR B 723 " --> pdb=" O LEU B 610 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE B 612 " --> pdb=" O THR B 723 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N PHE B 725 " --> pdb=" O ILE B 612 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 749 through 751 Processing sheet with id= E, first strand: chain 'A' and resid 55 through 58 removed outlier: 5.207A pdb=" N PHE A 40 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N LEU A 29 " --> pdb=" O PHE A 40 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 112 " --> pdb=" O ILE A 92 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU A 94 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N VAL A 110 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.333A pdb=" N LEU A 178 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG A 199 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N TYR A 180 " --> pdb=" O ARG A 199 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A 181 " --> pdb=" O ILE A 136 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N GLN A 138 " --> pdb=" O ALA A 181 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 601 through 603 removed outlier: 3.580A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 762 through 764 removed outlier: 6.325A pdb=" N MET A 609 " --> pdb=" O ALA A 743 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N VAL A 745 " --> pdb=" O MET A 609 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ILE A 611 " --> pdb=" O VAL A 745 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N LEU A 747 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N THR A 723 " --> pdb=" O LEU A 610 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE A 612 " --> pdb=" O THR A 723 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N PHE A 725 " --> pdb=" O ILE A 612 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 749 through 752 497 hydrogen bonds defined for protein. 1410 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: 3.15 Time building geometry restraints manager: 4.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 3181 1.34 - 1.48: 1487 1.48 - 1.62: 5732 1.62 - 1.76: 0 1.76 - 1.90: 99 Bond restraints: 10499 Sorted by residual: bond pdb=" C4 ADP A 903 " pdb=" C5 ADP A 903 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.03e+01 bond pdb=" C4 ADP B1002 " pdb=" C5 ADP B1002 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" N ILE A 66 " pdb=" CA ILE A 66 " ideal model delta sigma weight residual 1.460 1.494 -0.033 7.60e-03 1.73e+04 1.94e+01 bond pdb=" N ASN A 174 " pdb=" CA ASN A 174 " ideal model delta sigma weight residual 1.458 1.490 -0.032 7.40e-03 1.83e+04 1.88e+01 bond pdb=" N ARG B 199 " pdb=" CA ARG B 199 " ideal model delta sigma weight residual 1.453 1.489 -0.035 8.30e-03 1.45e+04 1.82e+01 ... (remaining 10494 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.83: 312 105.83 - 112.95: 5080 112.95 - 120.07: 5054 120.07 - 127.19: 3712 127.19 - 134.32: 67 Bond angle restraints: 14225 Sorted by residual: angle pdb=" CA PHE A 725 " pdb=" CB PHE A 725 " pdb=" CG PHE A 725 " ideal model delta sigma weight residual 113.80 120.22 -6.42 1.00e+00 1.00e+00 4.12e+01 angle pdb=" N PRO A 25 " pdb=" CA PRO A 25 " pdb=" C PRO A 25 " ideal model delta sigma weight residual 113.40 121.56 -8.16 1.34e+00 5.57e-01 3.71e+01 angle pdb=" C PRO B 231 " pdb=" CA PRO B 231 " pdb=" CB PRO B 231 " ideal model delta sigma weight residual 113.06 103.64 9.42 1.59e+00 3.96e-01 3.51e+01 angle pdb=" N GLU B 263 " pdb=" CA GLU B 263 " pdb=" C GLU B 263 " ideal model delta sigma weight residual 111.87 103.88 7.99 1.41e+00 5.03e-01 3.21e+01 angle pdb=" N PRO A 605 " pdb=" CA PRO A 605 " pdb=" C PRO A 605 " ideal model delta sigma weight residual 113.65 106.31 7.34 1.35e+00 5.49e-01 2.96e+01 ... (remaining 14220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 6287 35.45 - 70.91: 128 70.91 - 106.36: 15 106.36 - 141.82: 1 141.82 - 177.27: 2 Dihedral angle restraints: 6433 sinusoidal: 2634 harmonic: 3799 Sorted by residual: dihedral pdb=" O1B ADP B1002 " pdb=" O3A ADP B1002 " pdb=" PB ADP B1002 " pdb=" PA ADP B1002 " ideal model delta sinusoidal sigma weight residual -60.00 117.27 -177.27 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP B1002 " pdb=" O3A ADP B1002 " pdb=" PA ADP B1002 " pdb=" PB ADP B1002 " ideal model delta sinusoidal sigma weight residual -60.00 82.70 -142.70 1 2.00e+01 2.50e-03 4.31e+01 dihedral pdb=" C5' ADP B1002 " pdb=" O5' ADP B1002 " pdb=" PA ADP B1002 " pdb=" O2A ADP B1002 " ideal model delta sinusoidal sigma weight residual 300.00 173.49 126.52 1 2.00e+01 2.50e-03 3.83e+01 ... (remaining 6430 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 769 0.075 - 0.150: 567 0.150 - 0.226: 228 0.226 - 0.301: 65 0.301 - 0.376: 3 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CB ILE B 258 " pdb=" CA ILE B 258 " pdb=" CG1 ILE B 258 " pdb=" CG2 ILE B 258 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CA ILE B 258 " pdb=" N ILE B 258 " pdb=" C ILE B 258 " pdb=" CB ILE B 258 " both_signs ideal model delta sigma weight residual False 2.43 2.76 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA LEU A 133 " pdb=" N LEU A 133 " pdb=" C LEU A 133 " pdb=" CB LEU A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 1629 not shown) Planarity restraints: 1852 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 336 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.85e+00 pdb=" C ALA B 336 " -0.045 2.00e-02 2.50e+03 pdb=" O ALA B 336 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY B 337 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 268 " 0.012 2.00e-02 2.50e+03 2.42e-02 5.84e+00 pdb=" C ILE B 268 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE B 268 " 0.016 2.00e-02 2.50e+03 pdb=" N MET B 269 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 250 " 0.011 2.00e-02 2.50e+03 2.36e-02 5.55e+00 pdb=" C THR B 250 " -0.041 2.00e-02 2.50e+03 pdb=" O THR B 250 " 0.015 2.00e-02 2.50e+03 pdb=" N THR B 251 " 0.014 2.00e-02 2.50e+03 ... (remaining 1849 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 11 2.42 - 3.04: 5694 3.04 - 3.66: 15981 3.66 - 4.28: 23241 4.28 - 4.90: 39360 Nonbonded interactions: 84287 Sorted by model distance: nonbonded pdb=" OG SER A 621 " pdb="MG MG A 902 " model vdw 1.798 2.170 nonbonded pdb=" OG SER B 621 " pdb="MG MG B1001 " model vdw 2.041 2.170 nonbonded pdb=" O ILE A 597 " pdb=" N6 ADP A 903 " model vdw 2.233 2.520 nonbonded pdb="MG MG A 902 " pdb=" O2 VO4 A 904 " model vdw 2.241 2.170 nonbonded pdb="MG MG B1001 " pdb=" O3 VO4 A 901 " model vdw 2.251 2.170 ... (remaining 84282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.040 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: 0.950 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 31.440 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 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 : 0.013 0.110 10499 Z= 0.854 Angle : 1.765 13.659 14225 Z= 1.349 Chirality : 0.112 0.376 1632 Planarity : 0.006 0.036 1852 Dihedral : 15.367 177.269 3975 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.09 % Allowed : 7.93 % Favored : 91.97 % 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: 2.70 (0.21), residues: 1301 helix: 3.41 (0.17), residues: 661 sheet: 0.89 (0.39), residues: 157 loop : -0.28 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 202 HIS 0.008 0.002 HIS B 760 PHE 0.030 0.004 PHE A 725 TYR 0.030 0.003 TYR A 31 ARG 0.008 0.001 ARG B 354 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 431 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 THR cc_start: 0.8830 (t) cc_final: 0.8545 (m) REVERT: B 180 TYR cc_start: 0.8306 (p90) cc_final: 0.7845 (p90) REVERT: B 208 THR cc_start: 0.7703 (m) cc_final: 0.6693 (m) REVERT: B 242 GLN cc_start: 0.8612 (tp40) cc_final: 0.8379 (tp-100) REVERT: B 349 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7926 (mt-10) REVERT: B 359 THR cc_start: 0.8523 (m) cc_final: 0.8263 (p) REVERT: B 420 ARG cc_start: 0.8173 (ttp80) cc_final: 0.7782 (ttp80) REVERT: B 538 HIS cc_start: 0.8824 (m-70) cc_final: 0.8286 (m90) REVERT: A 43 ASP cc_start: 0.8622 (m-30) cc_final: 0.8165 (m-30) REVERT: A 115 THR cc_start: 0.9224 (p) cc_final: 0.8984 (t) REVERT: A 125 LEU cc_start: 0.8096 (mt) cc_final: 0.7870 (mt) REVERT: A 129 GLN cc_start: 0.8667 (mm-40) cc_final: 0.8360 (mm-40) REVERT: A 204 PHE cc_start: 0.8104 (m-80) cc_final: 0.7802 (m-10) REVERT: A 275 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8476 (tpp-160) REVERT: A 739 MET cc_start: 0.8586 (ttp) cc_final: 0.8201 (ttt) REVERT: A 740 GLU cc_start: 0.8387 (tt0) cc_final: 0.8162 (mm-30) REVERT: A 752 HIS cc_start: 0.7925 (t-90) cc_final: 0.7594 (t-90) outliers start: 1 outliers final: 0 residues processed: 432 average time/residue: 0.3068 time to fit residues: 170.1581 Evaluate side-chains 206 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 102 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 391 GLN B 538 HIS B 590 GLN B 643 GLN B 728 HIS B 791 GLN A 430 ASN A 543 GLN A 683 ASN A 714 ASN A 744 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10499 Z= 0.217 Angle : 0.653 11.021 14225 Z= 0.323 Chirality : 0.042 0.171 1632 Planarity : 0.005 0.041 1852 Dihedral : 8.240 165.859 1469 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 4.06 % Allowed : 15.22 % Favored : 80.72 % 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: 2.11 (0.22), residues: 1301 helix: 2.78 (0.19), residues: 672 sheet: 0.95 (0.37), residues: 184 loop : -0.63 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 137 HIS 0.011 0.001 HIS B 752 PHE 0.015 0.002 PHE B 654 TYR 0.021 0.002 TYR B 623 ARG 0.006 0.001 ARG A 667 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 194 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 GLN cc_start: 0.8561 (tp40) cc_final: 0.8060 (mp10) REVERT: B 180 TYR cc_start: 0.8487 (p90) cc_final: 0.7724 (p90) REVERT: B 349 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8004 (mt-10) REVERT: B 359 THR cc_start: 0.8548 (OUTLIER) cc_final: 0.8339 (p) REVERT: B 517 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8494 (pptt) REVERT: B 538 HIS cc_start: 0.8570 (m90) cc_final: 0.8054 (m170) REVERT: B 561 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8191 (mmm160) REVERT: B 592 LEU cc_start: 0.8851 (tp) cc_final: 0.8535 (tp) REVERT: B 688 SER cc_start: 0.8516 (m) cc_final: 0.8119 (m) REVERT: B 737 GLU cc_start: 0.7986 (pm20) cc_final: 0.7509 (tm-30) REVERT: A 43 ASP cc_start: 0.8804 (m-30) cc_final: 0.8554 (m-30) REVERT: A 86 GLN cc_start: 0.8360 (mt0) cc_final: 0.7700 (mp10) REVERT: A 115 THR cc_start: 0.9234 (p) cc_final: 0.9027 (t) REVERT: A 129 GLN cc_start: 0.8788 (mm-40) cc_final: 0.8277 (mm110) REVERT: A 184 PHE cc_start: 0.7549 (t80) cc_final: 0.7319 (t80) REVERT: A 275 ARG cc_start: 0.8731 (mmm160) cc_final: 0.8482 (ttm-80) REVERT: A 278 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: A 671 MET cc_start: 0.8574 (mmm) cc_final: 0.8311 (tpp) REVERT: A 739 MET cc_start: 0.8668 (ttp) cc_final: 0.8264 (ttt) REVERT: A 740 GLU cc_start: 0.8613 (tt0) cc_final: 0.8327 (mp0) outliers start: 44 outliers final: 23 residues processed: 221 average time/residue: 0.2262 time to fit residues: 70.2672 Evaluate side-chains 179 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 153 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 278 GLU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 551 GLU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 723 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 99 optimal weight: 3.9990 chunk 81 optimal weight: 7.9990 chunk 32 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 128 optimal weight: 20.0000 chunk 106 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 95 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 174 ASN A 430 ASN A 626 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 10499 Z= 0.292 Angle : 0.630 7.511 14225 Z= 0.311 Chirality : 0.043 0.298 1632 Planarity : 0.004 0.037 1852 Dihedral : 7.944 157.679 1469 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 4.24 % Allowed : 16.33 % Favored : 79.43 % 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: 1.67 (0.22), residues: 1301 helix: 2.43 (0.19), residues: 673 sheet: 0.54 (0.37), residues: 181 loop : -0.75 (0.25), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP B 436 HIS 0.007 0.001 HIS B 752 PHE 0.019 0.002 PHE B 184 TYR 0.022 0.002 TYR B 623 ARG 0.006 0.001 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 167 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 PHE cc_start: 0.6173 (m-10) cc_final: 0.5339 (m-10) REVERT: B 171 GLN cc_start: 0.8530 (tp40) cc_final: 0.8003 (mp10) REVERT: B 187 MET cc_start: 0.8223 (tmm) cc_final: 0.8008 (tmm) REVERT: B 196 LEU cc_start: 0.7803 (tt) cc_final: 0.7048 (mp) REVERT: B 349 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8079 (mt-10) REVERT: B 359 THR cc_start: 0.8644 (OUTLIER) cc_final: 0.8367 (p) REVERT: B 365 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9278 (mp) REVERT: B 517 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8333 (pptt) REVERT: B 538 HIS cc_start: 0.8618 (m90) cc_final: 0.8193 (m90) REVERT: B 557 ASN cc_start: 0.8771 (OUTLIER) cc_final: 0.8451 (t0) REVERT: B 592 LEU cc_start: 0.8973 (tp) cc_final: 0.8614 (tt) REVERT: A 13 MET cc_start: 0.8685 (ppp) cc_final: 0.8317 (ppp) REVERT: A 43 ASP cc_start: 0.8867 (m-30) cc_final: 0.8640 (m-30) REVERT: A 129 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8176 (mm110) REVERT: A 149 ASP cc_start: 0.7898 (t0) cc_final: 0.7538 (t0) REVERT: A 152 SER cc_start: 0.8513 (p) cc_final: 0.8166 (t) REVERT: A 184 PHE cc_start: 0.7608 (t80) cc_final: 0.7313 (t80) REVERT: A 275 ARG cc_start: 0.8833 (mmm160) cc_final: 0.8499 (ttm-80) REVERT: A 671 MET cc_start: 0.8647 (mmm) cc_final: 0.8205 (mmm) REVERT: A 739 MET cc_start: 0.8687 (ttp) cc_final: 0.8274 (ttt) REVERT: A 740 GLU cc_start: 0.8538 (tt0) cc_final: 0.8220 (mm-30) outliers start: 46 outliers final: 33 residues processed: 196 average time/residue: 0.2265 time to fit residues: 63.2039 Evaluate side-chains 180 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 143 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 365 LEU Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 701 THR Chi-restraints excluded: chain A residue 707 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 117 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 chunk 80 optimal weight: 0.3980 chunk 119 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 113 optimal weight: 0.9980 chunk 34 optimal weight: 9.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10499 Z= 0.228 Angle : 0.584 8.127 14225 Z= 0.285 Chirality : 0.040 0.164 1632 Planarity : 0.004 0.039 1852 Dihedral : 7.762 156.456 1469 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 4.06 % Allowed : 16.97 % Favored : 78.97 % 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: 1.50 (0.23), residues: 1301 helix: 2.40 (0.20), residues: 673 sheet: 0.26 (0.37), residues: 178 loop : -0.91 (0.25), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 202 HIS 0.005 0.001 HIS B 752 PHE 0.023 0.002 PHE B 143 TYR 0.020 0.002 TYR B 623 ARG 0.005 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 161 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 GLN cc_start: 0.8526 (tp40) cc_final: 0.8089 (mp10) REVERT: B 178 LEU cc_start: 0.8536 (tt) cc_final: 0.8277 (mp) REVERT: B 196 LEU cc_start: 0.7922 (tt) cc_final: 0.7058 (mp) REVERT: B 269 MET cc_start: 0.8102 (mtm) cc_final: 0.7899 (mtp) REVERT: B 349 GLU cc_start: 0.8427 (mm-30) cc_final: 0.8009 (mt-10) REVERT: B 359 THR cc_start: 0.8869 (OUTLIER) cc_final: 0.8539 (p) REVERT: B 517 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8304 (pptt) REVERT: B 538 HIS cc_start: 0.8482 (m90) cc_final: 0.8066 (m90) REVERT: B 557 ASN cc_start: 0.8776 (OUTLIER) cc_final: 0.8480 (t0) REVERT: B 592 LEU cc_start: 0.8986 (tp) cc_final: 0.8592 (tt) REVERT: B 693 ASP cc_start: 0.7908 (t0) cc_final: 0.7662 (t70) REVERT: B 748 ASP cc_start: 0.7577 (t0) cc_final: 0.6940 (t0) REVERT: A 13 MET cc_start: 0.8662 (ppp) cc_final: 0.8151 (ppp) REVERT: A 41 TYR cc_start: 0.8683 (m-80) cc_final: 0.8406 (m-80) REVERT: A 43 ASP cc_start: 0.8977 (m-30) cc_final: 0.8737 (m-30) REVERT: A 129 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8153 (mm110) REVERT: A 149 ASP cc_start: 0.7892 (t0) cc_final: 0.7635 (t0) REVERT: A 152 SER cc_start: 0.8374 (p) cc_final: 0.8082 (t) REVERT: A 184 PHE cc_start: 0.7529 (t80) cc_final: 0.7166 (t80) REVERT: A 275 ARG cc_start: 0.8888 (mmm160) cc_final: 0.8501 (tpp-160) REVERT: A 646 GLU cc_start: 0.8780 (mp0) cc_final: 0.8467 (mp0) REVERT: A 671 MET cc_start: 0.8658 (mmm) cc_final: 0.8334 (tpp) REVERT: A 714 ASN cc_start: 0.8741 (t0) cc_final: 0.8415 (t0) REVERT: A 739 MET cc_start: 0.8686 (ttp) cc_final: 0.8415 (ttm) REVERT: A 740 GLU cc_start: 0.8551 (tt0) cc_final: 0.8318 (mm-30) outliers start: 44 outliers final: 31 residues processed: 191 average time/residue: 0.2241 time to fit residues: 61.0818 Evaluate side-chains 181 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 514 LEU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 701 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 105 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 108 optimal weight: 0.4980 chunk 87 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 64 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN A 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10499 Z= 0.248 Angle : 0.606 12.555 14225 Z= 0.292 Chirality : 0.041 0.300 1632 Planarity : 0.004 0.038 1852 Dihedral : 7.610 155.925 1469 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.15 % Favored : 97.77 % Rotamer: Outliers : 4.34 % Allowed : 18.36 % Favored : 77.31 % 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: 1.35 (0.23), residues: 1301 helix: 2.34 (0.20), residues: 670 sheet: 0.01 (0.38), residues: 174 loop : -0.99 (0.25), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP B 436 HIS 0.004 0.001 HIS B 752 PHE 0.016 0.002 PHE B 204 TYR 0.020 0.001 TYR B 623 ARG 0.006 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 162 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 MET cc_start: 0.8580 (mmm) cc_final: 0.7370 (tmm) REVERT: B 171 GLN cc_start: 0.8431 (tp40) cc_final: 0.7991 (mt0) REVERT: B 196 LEU cc_start: 0.7855 (tt) cc_final: 0.6937 (mp) REVERT: B 325 GLN cc_start: 0.8312 (mt0) cc_final: 0.8105 (mt0) REVERT: B 359 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8573 (p) REVERT: B 361 ARG cc_start: 0.8041 (OUTLIER) cc_final: 0.7840 (mmt90) REVERT: B 517 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8322 (pptt) REVERT: B 538 HIS cc_start: 0.8538 (m90) cc_final: 0.8153 (m90) REVERT: B 557 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8508 (t0) REVERT: B 592 LEU cc_start: 0.9011 (tp) cc_final: 0.8633 (tp) REVERT: B 734 GLN cc_start: 0.8537 (pt0) cc_final: 0.8332 (pm20) REVERT: B 748 ASP cc_start: 0.7645 (t0) cc_final: 0.7181 (t0) REVERT: A 13 MET cc_start: 0.8697 (ppp) cc_final: 0.8377 (ppp) REVERT: A 41 TYR cc_start: 0.8823 (m-80) cc_final: 0.8438 (m-80) REVERT: A 43 ASP cc_start: 0.9001 (m-30) cc_final: 0.8766 (m-30) REVERT: A 94 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8140 (pp20) REVERT: A 129 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8194 (mm110) REVERT: A 149 ASP cc_start: 0.7884 (t0) cc_final: 0.7608 (t0) REVERT: A 152 SER cc_start: 0.8408 (p) cc_final: 0.8023 (t) REVERT: A 275 ARG cc_start: 0.8910 (mmm160) cc_final: 0.8679 (tpp-160) REVERT: A 671 MET cc_start: 0.8701 (mmm) cc_final: 0.8214 (tpp) REVERT: A 739 MET cc_start: 0.8700 (ttp) cc_final: 0.8409 (ttm) REVERT: A 740 GLU cc_start: 0.8522 (tt0) cc_final: 0.8293 (mm-30) outliers start: 47 outliers final: 32 residues processed: 191 average time/residue: 0.2180 time to fit residues: 58.9515 Evaluate side-chains 181 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 701 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 126 optimal weight: 0.1980 chunk 105 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 10 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.5266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10499 Z= 0.185 Angle : 0.571 9.202 14225 Z= 0.276 Chirality : 0.040 0.179 1632 Planarity : 0.004 0.035 1852 Dihedral : 7.424 156.087 1469 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.92 % Favored : 98.00 % Rotamer: Outliers : 3.97 % Allowed : 18.91 % Favored : 77.12 % 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: 1.37 (0.23), residues: 1301 helix: 2.34 (0.20), residues: 678 sheet: -0.02 (0.39), residues: 174 loop : -0.98 (0.26), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 202 HIS 0.004 0.001 HIS B 752 PHE 0.010 0.001 PHE B 184 TYR 0.015 0.001 TYR B 623 ARG 0.006 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 159 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 166 MET cc_start: 0.8567 (mmm) cc_final: 0.7316 (tmm) REVERT: B 171 GLN cc_start: 0.8552 (tp40) cc_final: 0.8011 (mp10) REVERT: B 196 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.6990 (mp) REVERT: B 325 GLN cc_start: 0.8294 (mt0) cc_final: 0.8075 (mt0) REVERT: B 359 THR cc_start: 0.8877 (OUTLIER) cc_final: 0.8539 (p) REVERT: B 517 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8302 (pptt) REVERT: B 538 HIS cc_start: 0.8555 (m90) cc_final: 0.8230 (m90) REVERT: B 557 ASN cc_start: 0.8789 (OUTLIER) cc_final: 0.8499 (t0) REVERT: B 592 LEU cc_start: 0.9004 (tp) cc_final: 0.8611 (tp) REVERT: B 734 GLN cc_start: 0.8497 (pt0) cc_final: 0.8021 (pm20) REVERT: B 748 ASP cc_start: 0.7581 (t0) cc_final: 0.7120 (t0) REVERT: A 13 MET cc_start: 0.8473 (ppp) cc_final: 0.8168 (ppp) REVERT: A 41 TYR cc_start: 0.8826 (m-80) cc_final: 0.8260 (m-80) REVERT: A 43 ASP cc_start: 0.9063 (m-30) cc_final: 0.8846 (m-30) REVERT: A 94 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8129 (pp20) REVERT: A 129 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8198 (mm110) REVERT: A 275 ARG cc_start: 0.8923 (mmm160) cc_final: 0.8578 (tpp-160) REVERT: A 671 MET cc_start: 0.8723 (mmm) cc_final: 0.8236 (tpp) REVERT: A 731 GLU cc_start: 0.8584 (tp30) cc_final: 0.8384 (tp30) REVERT: A 739 MET cc_start: 0.8711 (ttp) cc_final: 0.8466 (ttm) REVERT: A 740 GLU cc_start: 0.8495 (tt0) cc_final: 0.8144 (mm-30) REVERT: A 794 ARG cc_start: 0.8024 (mtm180) cc_final: 0.7546 (mtm180) outliers start: 43 outliers final: 30 residues processed: 189 average time/residue: 0.2249 time to fit residues: 59.8966 Evaluate side-chains 179 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 145 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 557 ASN Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 701 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 122 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 106 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN A 543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 10499 Z= 0.301 Angle : 0.631 10.126 14225 Z= 0.303 Chirality : 0.042 0.421 1632 Planarity : 0.004 0.036 1852 Dihedral : 7.432 152.592 1469 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.61 % Favored : 97.31 % Rotamer: Outliers : 4.52 % Allowed : 19.10 % Favored : 76.38 % 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: 1.27 (0.23), residues: 1301 helix: 2.23 (0.20), residues: 673 sheet: -0.12 (0.39), residues: 174 loop : -0.89 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 202 HIS 0.004 0.001 HIS B 760 PHE 0.013 0.002 PHE B 654 TYR 0.020 0.002 TYR B 623 ARG 0.007 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 144 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 MET cc_start: 0.8554 (mmm) cc_final: 0.7446 (tmm) REVERT: B 171 GLN cc_start: 0.8540 (tp40) cc_final: 0.8030 (mp10) REVERT: B 196 LEU cc_start: 0.7926 (tt) cc_final: 0.6987 (mp) REVERT: B 203 GLU cc_start: 0.8205 (tt0) cc_final: 0.7768 (tp30) REVERT: B 325 GLN cc_start: 0.8425 (mt0) cc_final: 0.8169 (mt0) REVERT: B 359 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8537 (p) REVERT: B 517 LYS cc_start: 0.8605 (OUTLIER) cc_final: 0.8309 (pptt) REVERT: B 538 HIS cc_start: 0.8602 (m90) cc_final: 0.8291 (m90) REVERT: B 592 LEU cc_start: 0.9017 (tp) cc_final: 0.8671 (tp) REVERT: B 609 MET cc_start: 0.8378 (tpp) cc_final: 0.8032 (tpp) REVERT: B 748 ASP cc_start: 0.7627 (t0) cc_final: 0.7330 (t0) REVERT: A 13 MET cc_start: 0.8488 (ppp) cc_final: 0.8148 (ppp) REVERT: A 41 TYR cc_start: 0.8862 (m-80) cc_final: 0.8384 (m-80) REVERT: A 43 ASP cc_start: 0.8935 (m-30) cc_final: 0.8694 (m-30) REVERT: A 94 GLU cc_start: 0.8330 (mt-10) cc_final: 0.8109 (pp20) REVERT: A 129 GLN cc_start: 0.8721 (mm-40) cc_final: 0.8121 (mm110) REVERT: A 275 ARG cc_start: 0.8927 (mmm160) cc_final: 0.8539 (tpp-160) REVERT: A 609 MET cc_start: 0.8497 (ttm) cc_final: 0.8005 (ttm) REVERT: A 671 MET cc_start: 0.8751 (mmm) cc_final: 0.8245 (tpp) REVERT: A 731 GLU cc_start: 0.8635 (tp30) cc_final: 0.8420 (tp30) REVERT: A 739 MET cc_start: 0.8735 (ttp) cc_final: 0.8476 (ttm) REVERT: A 740 GLU cc_start: 0.8488 (tt0) cc_final: 0.8110 (mm-30) outliers start: 49 outliers final: 40 residues processed: 177 average time/residue: 0.2256 time to fit residues: 56.5085 Evaluate side-chains 179 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 137 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 517 LYS Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain B residue 750 LEU Chi-restraints excluded: chain B residue 762 VAL Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 535 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 701 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 80 optimal weight: 0.1980 chunk 86 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 11 optimal weight: 6.9990 chunk 99 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 GLN A 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10499 Z= 0.221 Angle : 0.601 10.741 14225 Z= 0.285 Chirality : 0.041 0.262 1632 Planarity : 0.004 0.039 1852 Dihedral : 7.209 150.722 1469 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.00 % Favored : 97.92 % Rotamer: Outliers : 3.87 % Allowed : 20.39 % Favored : 75.74 % 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: 1.34 (0.23), residues: 1301 helix: 2.28 (0.20), residues: 673 sheet: -0.08 (0.40), residues: 169 loop : -0.86 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 202 HIS 0.003 0.001 HIS B 752 PHE 0.009 0.001 PHE B 654 TYR 0.017 0.001 TYR B 623 ARG 0.008 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 150 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 166 MET cc_start: 0.8565 (mmm) cc_final: 0.7780 (tmm) REVERT: B 171 GLN cc_start: 0.8517 (tp40) cc_final: 0.8004 (mp10) REVERT: B 196 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.6889 (mp) REVERT: B 325 GLN cc_start: 0.8365 (mt0) cc_final: 0.8094 (mt0) REVERT: B 359 THR cc_start: 0.8888 (OUTLIER) cc_final: 0.8539 (p) REVERT: B 538 HIS cc_start: 0.8621 (m90) cc_final: 0.8327 (m90) REVERT: B 592 LEU cc_start: 0.9022 (tp) cc_final: 0.8682 (tp) REVERT: B 609 MET cc_start: 0.8326 (tpp) cc_final: 0.7959 (tpp) REVERT: B 748 ASP cc_start: 0.7604 (t0) cc_final: 0.7330 (t0) REVERT: A 13 MET cc_start: 0.8477 (ppp) cc_final: 0.8177 (ppp) REVERT: A 41 TYR cc_start: 0.8853 (m-80) cc_final: 0.8341 (m-80) REVERT: A 43 ASP cc_start: 0.8968 (m-30) cc_final: 0.8722 (m-30) REVERT: A 94 GLU cc_start: 0.8315 (mt-10) cc_final: 0.8076 (pp20) REVERT: A 129 GLN cc_start: 0.8727 (mm-40) cc_final: 0.8152 (mm110) REVERT: A 275 ARG cc_start: 0.8844 (mmm160) cc_final: 0.8529 (tpp-160) REVERT: A 539 LEU cc_start: 0.8847 (tt) cc_final: 0.8568 (tt) REVERT: A 609 MET cc_start: 0.8449 (ttm) cc_final: 0.7974 (ttm) REVERT: A 671 MET cc_start: 0.8752 (mmm) cc_final: 0.8252 (tpp) REVERT: A 739 MET cc_start: 0.8741 (ttp) cc_final: 0.8477 (ttm) REVERT: A 740 GLU cc_start: 0.8496 (tt0) cc_final: 0.8126 (mm-30) REVERT: A 794 ARG cc_start: 0.8057 (mtm180) cc_final: 0.7639 (mtm180) outliers start: 42 outliers final: 34 residues processed: 179 average time/residue: 0.2268 time to fit residues: 57.2096 Evaluate side-chains 175 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 139 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 701 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 120 optimal weight: 9.9990 chunk 110 optimal weight: 0.8980 chunk 117 optimal weight: 20.0000 chunk 70 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 chunk 92 optimal weight: 0.0030 chunk 36 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 124 optimal weight: 7.9990 overall best weight: 2.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 ASN A 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10499 Z= 0.184 Angle : 0.603 10.864 14225 Z= 0.286 Chirality : 0.040 0.211 1632 Planarity : 0.004 0.040 1852 Dihedral : 7.095 164.085 1469 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 3.32 % Allowed : 21.49 % Favored : 75.18 % 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: 1.39 (0.23), residues: 1301 helix: 2.32 (0.20), residues: 678 sheet: -0.04 (0.38), residues: 184 loop : -0.90 (0.27), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 202 HIS 0.003 0.001 HIS B 752 PHE 0.011 0.001 PHE A 184 TYR 0.015 0.001 TYR B 623 ARG 0.008 0.000 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 151 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 MET cc_start: 0.8547 (mmm) cc_final: 0.7763 (tmm) REVERT: B 196 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.6848 (mp) REVERT: B 325 GLN cc_start: 0.8353 (mt0) cc_final: 0.8110 (mt0) REVERT: B 359 THR cc_start: 0.8843 (OUTLIER) cc_final: 0.8520 (p) REVERT: B 538 HIS cc_start: 0.8643 (m90) cc_final: 0.8348 (m90) REVERT: B 592 LEU cc_start: 0.9024 (tp) cc_final: 0.8674 (tp) REVERT: B 609 MET cc_start: 0.8350 (tpp) cc_final: 0.8030 (tpp) REVERT: B 748 ASP cc_start: 0.7597 (t0) cc_final: 0.7325 (t0) REVERT: A 13 MET cc_start: 0.8329 (ppp) cc_final: 0.8047 (ppp) REVERT: A 41 TYR cc_start: 0.8836 (m-80) cc_final: 0.8377 (m-80) REVERT: A 43 ASP cc_start: 0.8992 (m-30) cc_final: 0.8748 (m-30) REVERT: A 94 GLU cc_start: 0.8215 (mt-10) cc_final: 0.8008 (pp20) REVERT: A 129 GLN cc_start: 0.8719 (mm-40) cc_final: 0.8134 (mm110) REVERT: A 275 ARG cc_start: 0.8869 (mmm160) cc_final: 0.8546 (tpp-160) REVERT: A 539 LEU cc_start: 0.8843 (tt) cc_final: 0.8558 (tt) REVERT: A 609 MET cc_start: 0.8375 (ttm) cc_final: 0.7936 (ttm) REVERT: A 671 MET cc_start: 0.8760 (mmm) cc_final: 0.8449 (tpp) REVERT: A 717 ASN cc_start: 0.9106 (t0) cc_final: 0.8829 (t0) REVERT: A 739 MET cc_start: 0.8751 (ttp) cc_final: 0.8488 (ttm) REVERT: A 740 GLU cc_start: 0.8543 (tt0) cc_final: 0.8182 (mm-30) REVERT: A 794 ARG cc_start: 0.8081 (mtm180) cc_final: 0.7678 (mtm180) outliers start: 36 outliers final: 30 residues processed: 175 average time/residue: 0.2306 time to fit residues: 57.6965 Evaluate side-chains 173 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 701 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 130 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 10 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 110 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 214 ASN B 557 ASN A 430 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.5786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 10499 Z= 0.337 Angle : 0.664 11.279 14225 Z= 0.318 Chirality : 0.042 0.186 1632 Planarity : 0.005 0.089 1852 Dihedral : 7.276 162.799 1469 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.84 % Favored : 97.08 % Rotamer: Outliers : 3.32 % Allowed : 21.77 % Favored : 74.91 % 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: 1.15 (0.23), residues: 1301 helix: 2.12 (0.20), residues: 673 sheet: -0.31 (0.38), residues: 174 loop : -0.89 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP A 202 HIS 0.004 0.001 HIS A 728 PHE 0.013 0.002 PHE A 184 TYR 0.020 0.002 TYR B 623 ARG 0.018 0.001 ARG A 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2602 Ramachandran restraints generated. 1301 Oldfield, 0 Emsley, 1301 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 166 MET cc_start: 0.8596 (mmm) cc_final: 0.8092 (tmm) REVERT: B 180 TYR cc_start: 0.8503 (p90) cc_final: 0.7245 (p90) REVERT: B 196 LEU cc_start: 0.7888 (tt) cc_final: 0.6870 (mp) REVERT: B 198 ARG cc_start: 0.8869 (OUTLIER) cc_final: 0.8611 (mtm180) REVERT: B 325 GLN cc_start: 0.8516 (mt0) cc_final: 0.8271 (mt0) REVERT: B 359 THR cc_start: 0.8903 (OUTLIER) cc_final: 0.8529 (p) REVERT: B 538 HIS cc_start: 0.8635 (m90) cc_final: 0.8333 (m90) REVERT: B 592 LEU cc_start: 0.9055 (tp) cc_final: 0.8721 (tp) REVERT: B 609 MET cc_start: 0.8421 (tpp) cc_final: 0.8053 (tpp) REVERT: B 748 ASP cc_start: 0.7651 (t0) cc_final: 0.7449 (t0) REVERT: A 13 MET cc_start: 0.8435 (ppp) cc_final: 0.8069 (ppp) REVERT: A 41 TYR cc_start: 0.8871 (m-80) cc_final: 0.8408 (m-80) REVERT: A 43 ASP cc_start: 0.8948 (m-30) cc_final: 0.8721 (m-30) REVERT: A 94 GLU cc_start: 0.8233 (mt-10) cc_final: 0.8014 (pp20) REVERT: A 129 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8192 (mm110) REVERT: A 149 ASP cc_start: 0.7695 (t0) cc_final: 0.7441 (t0) REVERT: A 275 ARG cc_start: 0.8803 (mmm160) cc_final: 0.8495 (tpp-160) REVERT: A 609 MET cc_start: 0.8486 (ttm) cc_final: 0.8004 (ttm) REVERT: A 671 MET cc_start: 0.8777 (mmm) cc_final: 0.8322 (tpp) REVERT: A 717 ASN cc_start: 0.9097 (t0) cc_final: 0.8850 (t0) REVERT: A 739 MET cc_start: 0.8735 (ttp) cc_final: 0.8474 (ttm) REVERT: A 740 GLU cc_start: 0.8509 (tt0) cc_final: 0.8147 (mm-30) outliers start: 36 outliers final: 32 residues processed: 163 average time/residue: 0.2048 time to fit residues: 48.4263 Evaluate side-chains 170 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 136 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 149 ASP Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 511 ASP Chi-restraints excluded: chain B residue 535 LEU Chi-restraints excluded: chain B residue 569 CYS Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 701 THR Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 711 CYS Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 130 ASP Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 545 SER Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 686 GLU Chi-restraints excluded: chain A residue 701 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 31 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 43 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 5 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 430 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.076835 restraints weight = 23698.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.079397 restraints weight = 12216.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.081141 restraints weight = 7528.293| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10499 Z= 0.235 Angle : 0.625 10.888 14225 Z= 0.297 Chirality : 0.041 0.179 1632 Planarity : 0.004 0.058 1852 Dihedral : 7.216 165.427 1469 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.61 % Favored : 97.31 % Rotamer: Outliers : 3.69 % Allowed : 21.59 % Favored : 74.72 % 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: 1.23 (0.23), residues: 1301 helix: 2.17 (0.20), residues: 677 sheet: -0.24 (0.37), residues: 185 loop : -0.88 (0.28), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 202 HIS 0.003 0.001 HIS A 728 PHE 0.010 0.001 PHE A 184 TYR 0.017 0.001 TYR B 623 ARG 0.011 0.000 ARG A 172 =============================================================================== Job complete usr+sys time: 2047.92 seconds wall clock time: 37 minutes 46.28 seconds (2266.28 seconds total)