Starting phenix.real_space_refine on Fri Feb 14 18:15:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ou0_13071/02_2025/7ou0_13071.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ou0_13071/02_2025/7ou0_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/cci-nas-00/data/ceres_data/7ou0_13071/02_2025/7ou0_13071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ou0_13071/02_2025/7ou0_13071.map" model { file = "/net/cci-nas-00/data/ceres_data/7ou0_13071/02_2025/7ou0_13071.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ou0_13071/02_2025/7ou0_13071.cif" } 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. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.01, per 1000 atoms: 0.58 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.32 Conformation dependent library (CDL) restraints added in 1.4 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... Secondary structure from input PDB file: 54 helices and 8 sheets defined 55.2% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 186 through 191 removed outlier: 3.728A pdb=" N LEU B 189 " --> pdb=" O GLU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 204 Processing helix chain 'B' and resid 205 through 218 Processing helix chain 'B' and resid 230 through 248 Processing helix chain 'B' and resid 251 through 255 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 290 through 296 Processing helix chain 'B' and resid 300 through 313 Processing helix chain 'B' and resid 317 through 331 removed outlier: 3.696A pdb=" N LEU B 321 " --> pdb=" O ASP B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 346 Proline residue: B 340 - end of helix removed outlier: 3.639A pdb=" N GLY B 346 " --> pdb=" O LEU B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 357 Processing helix chain 'B' and resid 361 through 385 Proline residue: B 376 - end of helix removed outlier: 3.777A pdb=" N THR B 384 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL B 385 " --> pdb=" O GLN B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 398 removed outlier: 3.543A pdb=" N GLY B 398 " --> pdb=" O ARG B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 430 through 441 Processing helix chain 'B' and resid 512 through 536 Processing helix chain 'B' and resid 538 through 566 Processing helix chain 'B' and resid 585 through 592 removed outlier: 4.056A pdb=" N GLN B 590 " --> pdb=" O PRO B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 636 Processing helix chain 'B' and resid 668 through 684 Processing helix chain 'B' and resid 700 through 718 Processing helix chain 'B' and resid 731 through 733 No H-bonds generated for 'chain 'B' and resid 731 through 733' Processing helix chain 'B' and resid 734 through 739 removed outlier: 4.019A pdb=" N LYS B 738 " --> pdb=" O GLN B 734 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 780 Processing helix chain 'B' and resid 782 through 799 Processing helix chain 'A' and resid 11 through 24 Processing helix chain 'A' and resid 41 through 52 removed outlier: 3.610A pdb=" N LYS A 45 " --> pdb=" O TYR A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 87 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 205 through 218 Processing helix chain 'A' and resid 230 through 249 Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 290 through 296 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 317 through 332 Processing helix chain 'A' and resid 334 through 346 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) removed outlier: 3.723A pdb=" N GLY A 346 " --> pdb=" O LEU A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 357 removed outlier: 3.637A pdb=" N ILE A 351 " --> pdb=" O ASP A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 385 Proline residue: A 376 - end of helix removed outlier: 3.509A pdb=" N THR A 384 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 398 removed outlier: 3.586A pdb=" N GLY A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 411 Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 430 through 442 Processing helix chain 'A' and resid 513 through 536 Processing helix chain 'A' and resid 538 through 566 Processing helix chain 'A' and resid 585 through 592 removed outlier: 3.788A pdb=" N GLN A 590 " --> pdb=" O PRO A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 619 through 635 removed outlier: 3.568A pdb=" N THR A 627 " --> pdb=" O TYR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 668 through 684 Processing helix chain 'A' and resid 700 through 718 Processing helix chain 'A' and resid 729 through 733 Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.621A pdb=" N LYS A 738 " --> pdb=" O GLN A 734 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 780 Processing helix chain 'A' and resid 782 through 800 Processing sheet with id=AA1, first strand: chain 'B' and resid 132 through 138 removed outlier: 3.508A pdb=" N ARG B 154 " --> pdb=" O ASP B 149 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 178 through 181 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) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 570 through 572 removed outlier: 3.639A pdb=" N LYS B 644 " --> pdb=" O THR B 581 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLU B 582 " --> pdb=" O ASN B 599 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN B 599 " --> pdb=" O GLU B 582 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 653 through 656 removed outlier: 6.223A pdb=" N PHE B 654 " --> pdb=" O LEU B 691 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASP B 693 " --> pdb=" O PHE B 654 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ARG B 656 " --> pdb=" O ASP B 693 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LEU B 610 " --> pdb=" O PHE B 725 " (cutoff:3.500A) 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: 8.450A pdb=" N ALA B 749 " --> pdb=" O THR B 613 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER B 761 " --> pdb=" O ASP B 748 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N LEU B 750 " --> pdb=" O MET B 759 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N MET B 759 " --> pdb=" O LEU B 750 " (cutoff:3.500A) Processing sheet with id=AA5, 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=AA6, 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=AA7, first strand: chain 'A' and resid 571 through 572 removed outlier: 6.313A pdb=" N THR A 571 " --> pdb=" O ILE A 647 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS A 644 " --> pdb=" O THR A 581 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU A 582 " --> pdb=" O ASN A 599 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN A 599 " --> pdb=" O GLU A 582 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 653 through 656 removed outlier: 6.132A pdb=" N PHE A 654 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASP A 693 " --> pdb=" O PHE A 654 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N ARG A 656 " --> pdb=" O ASP A 693 " (cutoff:3.500A) 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: 8.011A pdb=" N ASN A 744 " --> pdb=" O GLN A 763 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLN A 763 " --> pdb=" O ASN A 744 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS A 746 " --> pdb=" O SER A 761 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N SER A 761 " --> pdb=" O HIS A 746 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ASP A 748 " --> pdb=" O MET A 759 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1641 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: 3.62 Time building geometry restraints manager: 2.72 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: 0.00 - 2.73: 12504 2.73 - 5.46: 1658 5.46 - 8.20: 46 8.20 - 10.93: 15 10.93 - 13.66: 2 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: 5662 3.04 - 3.66: 15928 3.66 - 4.28: 23103 4.28 - 4.90: 39303 Nonbonded interactions: 84007 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 3.120 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 84002 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.050 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 25.390 Find NCS groups from input model: 0.090 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.060 ------------------------------------------------------------------------------- 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= 0.850 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 to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 1.202 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: 0.3154 time to fit residues: 174.6960 Evaluate side-chains 206 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.148 ------------------------------------------------------------------------------- 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: 7.9990 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 118 optimal weight: 3.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 538 HIS B 590 GLN B 643 GLN B 752 HIS B 791 GLN A 430 ASN A 543 GLN A 683 ASN A 714 ASN A 734 GLN A 744 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.103722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.089669 restraints weight = 21674.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.092670 restraints weight = 10475.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.094641 restraints weight = 6145.893| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3867 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= 0.221 Angle : 0.675 10.904 14225 Z= 0.337 Chirality : 0.043 0.172 1632 Planarity : 0.005 0.045 1852 Dihedral : 8.233 172.668 1469 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.97 % Allowed : 14.48 % Favored : 81.55 % 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: 2.18 (0.22), residues: 1301 helix: 2.82 (0.19), residues: 680 sheet: 0.78 (0.36), residues: 200 loop : -0.59 (0.25), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 202 HIS 0.011 0.001 HIS B 752 PHE 0.017 0.002 PHE B 184 TYR 0.019 0.002 TYR B 623 ARG 0.007 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 243 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 200 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 GLN cc_start: 0.8372 (tp40) cc_final: 0.8141 (mp10) REVERT: B 180 TYR cc_start: 0.7891 (p90) cc_final: 0.7480 (p90) REVERT: B 405 ASP cc_start: 0.7974 (t70) cc_final: 0.7685 (t70) REVERT: B 434 ASP cc_start: 0.7410 (m-30) cc_final: 0.7180 (m-30) REVERT: B 517 LYS cc_start: 0.8906 (OUTLIER) cc_final: 0.8390 (pptt) REVERT: B 538 HIS cc_start: 0.8256 (m90) cc_final: 0.7609 (m170) REVERT: B 688 SER cc_start: 0.8689 (m) cc_final: 0.8291 (m) REVERT: A 43 ASP cc_start: 0.8057 (m-30) cc_final: 0.7806 (m-30) REVERT: A 115 THR cc_start: 0.9154 (p) cc_final: 0.8872 (t) REVERT: A 129 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8068 (mm110) REVERT: A 313 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7737 (mmm) REVERT: A 323 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 739 MET cc_start: 0.7721 (ttp) cc_final: 0.7378 (ttm) outliers start: 43 outliers final: 22 residues processed: 225 average time/residue: 0.2425 time to fit residues: 75.2455 Evaluate side-chains 175 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 151 time to evaluate : 1.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 273 THR 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 723 THR 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 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 313 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 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 Chi-restraints excluded: chain A residue 734 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 66 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 92 optimal weight: 0.9980 chunk 69 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 116 optimal weight: 9.9990 chunk 115 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN A 734 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.101329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.087449 restraints weight = 22243.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.090347 restraints weight = 10971.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092276 restraints weight = 6520.386| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.4493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 10499 Z= 0.234 Angle : 0.621 7.803 14225 Z= 0.308 Chirality : 0.042 0.337 1632 Planarity : 0.004 0.044 1852 Dihedral : 7.874 167.062 1469 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.51 % Allowed : 16.61 % Favored : 79.89 % 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: 1.99 (0.23), residues: 1301 helix: 2.72 (0.19), residues: 681 sheet: 0.48 (0.36), residues: 195 loop : -0.66 (0.25), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 436 HIS 0.004 0.001 HIS A 254 PHE 0.016 0.002 PHE B 184 TYR 0.019 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 217 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 179 time to evaluate : 1.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 143 PHE cc_start: 0.6534 (m-10) cc_final: 0.5139 (m-10) REVERT: B 171 GLN cc_start: 0.8299 (tp40) cc_final: 0.7948 (mp10) REVERT: B 180 TYR cc_start: 0.7613 (p90) cc_final: 0.6492 (p90) REVERT: B 196 LEU cc_start: 0.7413 (tt) cc_final: 0.6826 (mp) REVERT: B 269 MET cc_start: 0.8010 (mtm) cc_final: 0.7805 (mtp) REVERT: B 405 ASP cc_start: 0.8261 (t70) cc_final: 0.7237 (t70) REVERT: B 434 ASP cc_start: 0.7401 (m-30) cc_final: 0.7077 (m-30) REVERT: B 517 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8288 (pptt) REVERT: B 538 HIS cc_start: 0.8323 (m90) cc_final: 0.7723 (m90) REVERT: B 561 ARG cc_start: 0.8531 (mmm160) cc_final: 0.7985 (mmm160) REVERT: B 709 TRP cc_start: 0.7967 (t-100) cc_final: 0.7600 (t-100) REVERT: A 13 MET cc_start: 0.8206 (ppp) cc_final: 0.7873 (ppp) REVERT: A 43 ASP cc_start: 0.8102 (m-30) cc_final: 0.7859 (m-30) REVERT: A 115 THR cc_start: 0.9159 (p) cc_final: 0.8870 (t) REVERT: A 129 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8077 (mm110) REVERT: A 149 ASP cc_start: 0.7388 (t0) cc_final: 0.7023 (t0) REVERT: A 152 SER cc_start: 0.8423 (p) cc_final: 0.8049 (t) REVERT: A 313 MET cc_start: 0.8081 (OUTLIER) cc_final: 0.7618 (mmm) REVERT: A 319 ARG cc_start: 0.6928 (tpp-160) cc_final: 0.6726 (tpp-160) REVERT: A 671 MET cc_start: 0.8248 (tpp) cc_final: 0.8003 (tpp) REVERT: A 714 ASN cc_start: 0.8649 (t0) cc_final: 0.8308 (t0) REVERT: A 739 MET cc_start: 0.7767 (ttp) cc_final: 0.7259 (ttm) outliers start: 38 outliers final: 25 residues processed: 200 average time/residue: 0.2420 time to fit residues: 67.4580 Evaluate side-chains 178 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 151 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 378 LEU 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 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 701 THR 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 95 GLN Chi-restraints excluded: chain A residue 111 VAL 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 313 MET Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 657 VAL 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 57 optimal weight: 6.9990 chunk 127 optimal weight: 0.1980 chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 54 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 5 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 112 optimal weight: 0.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 24 HIS A 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.093901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079656 restraints weight = 23293.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.082420 restraints weight = 11684.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.084219 restraints weight = 7055.990| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10499 Z= 0.241 Angle : 0.607 7.865 14225 Z= 0.298 Chirality : 0.041 0.170 1632 Planarity : 0.004 0.049 1852 Dihedral : 7.730 165.213 1469 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 3.51 % Allowed : 16.70 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.22), residues: 1301 helix: 2.64 (0.19), residues: 672 sheet: 0.34 (0.37), residues: 184 loop : -0.86 (0.25), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 202 HIS 0.003 0.001 HIS A 728 PHE 0.016 0.002 PHE B 184 TYR 0.019 0.001 TYR B 623 ARG 0.008 0.001 ARG B 409 *********************** 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 193 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 1.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 166 MET cc_start: 0.8411 (mmm) cc_final: 0.7009 (tmm) REVERT: B 170 LEU cc_start: 0.9115 (mp) cc_final: 0.8773 (mp) REVERT: B 171 GLN cc_start: 0.8294 (tp40) cc_final: 0.7948 (mp10) REVERT: B 180 TYR cc_start: 0.7951 (p90) cc_final: 0.6767 (p90) REVERT: B 196 LEU cc_start: 0.7597 (tt) cc_final: 0.6797 (mp) REVERT: B 434 ASP cc_start: 0.7859 (m-30) cc_final: 0.7437 (m-30) REVERT: B 517 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8284 (pptt) REVERT: B 538 HIS cc_start: 0.8400 (m90) cc_final: 0.7850 (m90) REVERT: B 592 LEU cc_start: 0.8956 (tp) cc_final: 0.8643 (tp) REVERT: A 13 MET cc_start: 0.8326 (ppp) cc_final: 0.7866 (ppp) REVERT: A 41 TYR cc_start: 0.8696 (m-80) cc_final: 0.8354 (m-80) REVERT: A 43 ASP cc_start: 0.8217 (m-30) cc_final: 0.7953 (m-30) REVERT: A 129 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7962 (mm110) REVERT: A 149 ASP cc_start: 0.7673 (t0) cc_final: 0.7358 (t0) REVERT: A 152 SER cc_start: 0.8207 (p) cc_final: 0.7869 (t) REVERT: A 281 GLN cc_start: 0.8962 (tt0) cc_final: 0.8662 (tt0) REVERT: A 313 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7666 (mmm) REVERT: A 408 GLU cc_start: 0.7706 (tt0) cc_final: 0.7305 (mt-10) REVERT: A 539 LEU cc_start: 0.8830 (tt) cc_final: 0.8526 (tt) REVERT: A 714 ASN cc_start: 0.8679 (t0) cc_final: 0.8321 (t0) REVERT: A 739 MET cc_start: 0.7910 (ttp) cc_final: 0.7438 (ttm) outliers start: 38 outliers final: 27 residues processed: 175 average time/residue: 0.2325 time to fit residues: 57.5936 Evaluate side-chains 176 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 2.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 259 THR 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 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 701 THR 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 111 VAL 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 313 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 430 ASN 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 592 LEU Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 686 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 48 optimal weight: 6.9990 chunk 85 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 chunk 9 optimal weight: 6.9990 chunk 40 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 242 GLN B 276 ASN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 381 GLN A 430 ASN A 682 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.076967 restraints weight = 23567.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.079482 restraints weight = 12225.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.081141 restraints weight = 7560.609| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10499 Z= 0.343 Angle : 0.657 11.772 14225 Z= 0.319 Chirality : 0.042 0.164 1632 Planarity : 0.005 0.041 1852 Dihedral : 7.725 162.038 1469 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 4.24 % Allowed : 17.25 % Favored : 78.51 % 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: 1.58 (0.23), residues: 1301 helix: 2.45 (0.19), residues: 668 sheet: 0.23 (0.39), residues: 171 loop : -0.77 (0.26), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 202 HIS 0.004 0.001 HIS B 760 PHE 0.015 0.002 PHE B 654 TYR 0.023 0.002 TYR B 623 ARG 0.010 0.001 ARG B 409 *********************** 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 203 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 1.191 Fit side-chains REVERT: B 166 MET cc_start: 0.8302 (mmm) cc_final: 0.7038 (tmm) REVERT: B 170 LEU cc_start: 0.9113 (mp) cc_final: 0.8523 (mp) REVERT: B 171 GLN cc_start: 0.8221 (tp40) cc_final: 0.7881 (mp10) REVERT: B 196 LEU cc_start: 0.7722 (tt) cc_final: 0.7135 (mp) REVERT: B 325 GLN cc_start: 0.8113 (mt0) cc_final: 0.7885 (mt0) REVERT: B 434 ASP cc_start: 0.7795 (m-30) cc_final: 0.7470 (m-30) REVERT: B 517 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8287 (pptt) REVERT: B 538 HIS cc_start: 0.8337 (m90) cc_final: 0.7837 (m90) REVERT: B 561 ARG cc_start: 0.8656 (mmm160) cc_final: 0.7873 (mmm160) REVERT: B 592 LEU cc_start: 0.8860 (tp) cc_final: 0.8584 (tt) REVERT: B 622 THR cc_start: 0.8955 (m) cc_final: 0.8667 (p) REVERT: A 13 MET cc_start: 0.8536 (ppp) cc_final: 0.8212 (ppp) REVERT: A 41 TYR cc_start: 0.8880 (m-80) cc_final: 0.8174 (m-80) REVERT: A 43 ASP cc_start: 0.8250 (m-30) cc_final: 0.8031 (m-30) REVERT: A 86 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7690 (mp10) REVERT: A 129 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7982 (mm110) REVERT: A 149 ASP cc_start: 0.7749 (t0) cc_final: 0.7436 (t0) REVERT: A 152 SER cc_start: 0.8243 (p) cc_final: 0.7918 (t) REVERT: A 281 GLN cc_start: 0.9002 (tt0) cc_final: 0.8662 (tt0) REVERT: A 313 MET cc_start: 0.8108 (OUTLIER) cc_final: 0.7721 (mmm) REVERT: A 714 ASN cc_start: 0.8646 (t0) cc_final: 0.8286 (t0) outliers start: 46 outliers final: 33 residues processed: 181 average time/residue: 0.2319 time to fit residues: 60.4543 Evaluate side-chains 183 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 198 ARG Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 378 LEU 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 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 701 THR 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 762 VAL Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 GLN 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 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 335 THR 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 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 120 optimal weight: 10.0000 chunk 68 optimal weight: 0.0020 chunk 69 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 overall best weight: 2.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 ASN ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.092280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.078647 restraints weight = 23509.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081233 restraints weight = 12044.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.082926 restraints weight = 7376.959| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.5292 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= 0.203 Angle : 0.597 9.147 14225 Z= 0.289 Chirality : 0.040 0.174 1632 Planarity : 0.004 0.040 1852 Dihedral : 7.518 160.337 1469 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.85 % Rotamer: Outliers : 3.41 % Allowed : 18.63 % Favored : 77.95 % 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: 1.66 (0.23), residues: 1301 helix: 2.55 (0.20), residues: 674 sheet: 0.17 (0.39), residues: 170 loop : -0.78 (0.26), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP B 436 HIS 0.003 0.001 HIS A 728 PHE 0.014 0.001 PHE B 184 TYR 0.018 0.001 TYR B 623 ARG 0.007 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 206 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 169 time to evaluate : 1.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 GLN cc_start: 0.8184 (tp40) cc_final: 0.7863 (mp10) REVERT: B 180 TYR cc_start: 0.7972 (p90) cc_final: 0.6867 (p90) REVERT: B 196 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.6801 (mp) REVERT: B 203 GLU cc_start: 0.7845 (tt0) cc_final: 0.7371 (tp30) REVERT: B 325 GLN cc_start: 0.7963 (mt0) cc_final: 0.7745 (mt0) REVERT: B 434 ASP cc_start: 0.7924 (m-30) cc_final: 0.7598 (m-30) REVERT: B 517 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.8178 (pptt) REVERT: B 538 HIS cc_start: 0.8345 (m90) cc_final: 0.7919 (m90) REVERT: B 592 LEU cc_start: 0.8893 (tp) cc_final: 0.8605 (tp) REVERT: B 622 THR cc_start: 0.8905 (m) cc_final: 0.8604 (p) REVERT: B 693 ASP cc_start: 0.7476 (t70) cc_final: 0.7218 (t70) REVERT: A 13 MET cc_start: 0.8515 (ppp) cc_final: 0.8120 (ppp) REVERT: A 41 TYR cc_start: 0.8850 (m-80) cc_final: 0.8205 (m-80) REVERT: A 43 ASP cc_start: 0.8344 (m-30) cc_final: 0.8096 (m-30) REVERT: A 86 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.7589 (mp10) REVERT: A 129 GLN cc_start: 0.8250 (mm-40) cc_final: 0.7956 (mm110) REVERT: A 149 ASP cc_start: 0.7645 (t0) cc_final: 0.7363 (t0) REVERT: A 152 SER cc_start: 0.8134 (p) cc_final: 0.7748 (t) REVERT: A 281 GLN cc_start: 0.9018 (tt0) cc_final: 0.8676 (tt0) REVERT: A 313 MET cc_start: 0.7963 (OUTLIER) cc_final: 0.7676 (mmm) REVERT: A 531 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8429 (tp) REVERT: A 671 MET cc_start: 0.8204 (tpp) cc_final: 0.7899 (tpt) REVERT: A 714 ASN cc_start: 0.8642 (t0) cc_final: 0.8293 (t0) REVERT: A 794 ARG cc_start: 0.7642 (mtm180) cc_final: 0.6808 (mtm110) outliers start: 37 outliers final: 26 residues processed: 190 average time/residue: 0.2403 time to fit residues: 64.1450 Evaluate side-chains 187 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 156 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR 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 252 LEU Chi-restraints excluded: chain B residue 259 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 640 VAL Chi-restraints excluded: chain B residue 690 VAL 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 39 LEU Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 430 ASN Chi-restraints excluded: chain A residue 441 ASP Chi-restraints excluded: chain A residue 527 LEU Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 657 VAL 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 51 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.077044 restraints weight = 23885.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.079546 restraints weight = 12370.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081217 restraints weight = 7671.537| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10499 Z= 0.310 Angle : 0.652 11.143 14225 Z= 0.314 Chirality : 0.042 0.166 1632 Planarity : 0.004 0.042 1852 Dihedral : 7.423 151.838 1469 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.23 % Favored : 97.69 % Rotamer: Outliers : 3.78 % Allowed : 19.19 % Favored : 77.03 % 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: 1.54 (0.23), residues: 1301 helix: 2.43 (0.20), residues: 680 sheet: -0.08 (0.39), residues: 170 loop : -0.75 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 202 HIS 0.003 0.001 HIS A 10 PHE 0.013 0.002 PHE B 654 TYR 0.022 0.001 TYR B 623 ARG 0.008 0.001 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 197 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 156 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 TYR cc_start: 0.7960 (p90) cc_final: 0.6878 (p90) REVERT: B 196 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.6858 (mp) REVERT: B 203 GLU cc_start: 0.7830 (tt0) cc_final: 0.7372 (tp30) REVERT: B 325 GLN cc_start: 0.8115 (mt0) cc_final: 0.7862 (mt0) REVERT: B 434 ASP cc_start: 0.7927 (m-30) cc_final: 0.7602 (m-30) REVERT: B 517 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8164 (pptt) REVERT: B 538 HIS cc_start: 0.8394 (m90) cc_final: 0.7994 (m90) REVERT: B 592 LEU cc_start: 0.8903 (tp) cc_final: 0.8606 (tt) REVERT: B 622 THR cc_start: 0.8983 (m) cc_final: 0.8704 (p) REVERT: B 693 ASP cc_start: 0.7612 (t70) cc_final: 0.7341 (t70) REVERT: A 13 MET cc_start: 0.8566 (ppp) cc_final: 0.8115 (ppp) REVERT: A 41 TYR cc_start: 0.8887 (m-80) cc_final: 0.8277 (m-80) REVERT: A 43 ASP cc_start: 0.8319 (m-30) cc_final: 0.8086 (m-30) REVERT: A 129 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7951 (mm110) REVERT: A 149 ASP cc_start: 0.7719 (t0) cc_final: 0.7406 (t0) REVERT: A 152 SER cc_start: 0.8188 (p) cc_final: 0.7848 (t) REVERT: A 281 GLN cc_start: 0.9035 (tt0) cc_final: 0.8672 (tt0) REVERT: A 313 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7809 (tpp) REVERT: A 531 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8456 (tp) REVERT: A 671 MET cc_start: 0.8229 (tpp) cc_final: 0.7943 (tpt) REVERT: A 714 ASN cc_start: 0.8607 (t0) cc_final: 0.8257 (t0) outliers start: 41 outliers final: 32 residues processed: 179 average time/residue: 0.2219 time to fit residues: 56.8740 Evaluate side-chains 182 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 146 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR 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 252 LEU Chi-restraints excluded: chain B residue 299 VAL 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 701 THR 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 68 MET Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 335 THR Chi-restraints excluded: chain A residue 441 ASP 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 535 LEU Chi-restraints excluded: chain A residue 592 LEU Chi-restraints excluded: chain A residue 657 VAL 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 22 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 84 optimal weight: 0.9980 chunk 109 optimal weight: 7.9990 chunk 125 optimal weight: 7.9990 chunk 9 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 2 optimal weight: 8.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.086438 restraints weight = 22484.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.089222 restraints weight = 11205.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091055 restraints weight = 6714.603| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10499 Z= 0.182 Angle : 0.611 11.373 14225 Z= 0.292 Chirality : 0.040 0.184 1632 Planarity : 0.004 0.040 1852 Dihedral : 7.261 151.870 1469 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.08 % Favored : 97.85 % Rotamer: Outliers : 2.86 % Allowed : 20.39 % Favored : 76.75 % 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: 1.68 (0.23), residues: 1301 helix: 2.56 (0.20), residues: 683 sheet: -0.21 (0.36), residues: 197 loop : -0.67 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP A 202 HIS 0.004 0.001 HIS A 728 PHE 0.012 0.001 PHE B 143 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 195 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 180 TYR cc_start: 0.7805 (p90) cc_final: 0.6774 (p90) REVERT: B 196 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.6743 (mp) REVERT: B 203 GLU cc_start: 0.7694 (tt0) cc_final: 0.7306 (tp30) REVERT: B 325 GLN cc_start: 0.8013 (mt0) cc_final: 0.7764 (mt0) REVERT: B 434 ASP cc_start: 0.7880 (m-30) cc_final: 0.7545 (m-30) REVERT: B 517 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8107 (pptt) REVERT: B 538 HIS cc_start: 0.8268 (m90) cc_final: 0.7871 (m90) REVERT: B 592 LEU cc_start: 0.8904 (tp) cc_final: 0.8654 (tp) REVERT: B 622 THR cc_start: 0.8876 (m) cc_final: 0.8622 (p) REVERT: B 693 ASP cc_start: 0.7686 (t70) cc_final: 0.7393 (t0) REVERT: A 13 MET cc_start: 0.8419 (ppp) cc_final: 0.8058 (ppp) REVERT: A 41 TYR cc_start: 0.8898 (m-80) cc_final: 0.8242 (m-80) REVERT: A 43 ASP cc_start: 0.8307 (m-30) cc_final: 0.8066 (m-30) REVERT: A 86 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7659 (mp10) REVERT: A 129 GLN cc_start: 0.8248 (mm-40) cc_final: 0.7961 (mm110) REVERT: A 281 GLN cc_start: 0.8987 (tt0) cc_final: 0.8724 (tt0) REVERT: A 313 MET cc_start: 0.7951 (OUTLIER) cc_final: 0.7710 (mmm) REVERT: A 531 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8405 (tp) REVERT: A 539 LEU cc_start: 0.9070 (tp) cc_final: 0.8838 (tp) REVERT: A 671 MET cc_start: 0.8155 (tpp) cc_final: 0.7941 (tpt) REVERT: A 714 ASN cc_start: 0.8489 (t0) cc_final: 0.8053 (t0) REVERT: A 738 LYS cc_start: 0.8525 (tttt) cc_final: 0.8205 (tttt) outliers start: 31 outliers final: 22 residues processed: 180 average time/residue: 0.2270 time to fit residues: 58.1817 Evaluate side-chains 179 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 213 LEU Chi-restraints excluded: chain B residue 259 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 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 GLN 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 215 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 335 THR 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 657 VAL 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 21 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 59 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 9 optimal weight: 7.9990 chunk 46 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.099897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.086375 restraints weight = 22493.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.089157 restraints weight = 11311.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090992 restraints weight = 6801.528| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5618 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= 0.209 Angle : 0.629 11.784 14225 Z= 0.304 Chirality : 0.040 0.178 1632 Planarity : 0.004 0.040 1852 Dihedral : 7.199 156.517 1469 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 2.95 % Allowed : 20.66 % 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: 1.62 (0.23), residues: 1301 helix: 2.50 (0.20), residues: 677 sheet: -0.18 (0.37), residues: 197 loop : -0.65 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP B 436 HIS 0.003 0.001 HIS B 760 PHE 0.029 0.001 PHE B 184 TYR 0.018 0.001 TYR B 623 ARG 0.009 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 189 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 TYR cc_start: 0.7765 (p90) cc_final: 0.6696 (p90) REVERT: B 196 LEU cc_start: 0.7543 (OUTLIER) cc_final: 0.6746 (mp) REVERT: B 203 GLU cc_start: 0.7711 (tt0) cc_final: 0.7330 (tp30) REVERT: B 221 ASP cc_start: 0.7610 (t70) cc_final: 0.7281 (t0) REVERT: B 325 GLN cc_start: 0.8065 (mt0) cc_final: 0.7774 (mt0) REVERT: B 434 ASP cc_start: 0.7879 (m-30) cc_final: 0.7570 (m-30) REVERT: B 517 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8019 (pptt) REVERT: B 538 HIS cc_start: 0.8271 (m90) cc_final: 0.7893 (m90) REVERT: B 592 LEU cc_start: 0.8913 (tp) cc_final: 0.8676 (tp) REVERT: B 622 THR cc_start: 0.8911 (m) cc_final: 0.8638 (p) REVERT: B 693 ASP cc_start: 0.7686 (t70) cc_final: 0.7401 (t0) REVERT: B 759 MET cc_start: 0.7174 (mtm) cc_final: 0.6882 (mtt) REVERT: A 13 MET cc_start: 0.8375 (ppp) cc_final: 0.8002 (ppp) REVERT: A 41 TYR cc_start: 0.8878 (m-80) cc_final: 0.8318 (m-80) REVERT: A 43 ASP cc_start: 0.8328 (m-30) cc_final: 0.8105 (m-30) REVERT: A 129 GLN cc_start: 0.8183 (mm-40) cc_final: 0.7886 (mm110) REVERT: A 184 PHE cc_start: 0.7563 (t80) cc_final: 0.7117 (t80) REVERT: A 281 GLN cc_start: 0.8998 (tt0) cc_final: 0.8721 (tt0) REVERT: A 539 LEU cc_start: 0.9078 (tp) cc_final: 0.8851 (tp) REVERT: A 671 MET cc_start: 0.8186 (tpp) cc_final: 0.7962 (tpt) REVERT: A 714 ASN cc_start: 0.8455 (t0) cc_final: 0.7986 (t0) outliers start: 32 outliers final: 24 residues processed: 176 average time/residue: 0.2276 time to fit residues: 56.9101 Evaluate side-chains 172 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 146 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 213 LEU 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 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 GLN 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 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 335 THR 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 592 LEU Chi-restraints excluded: chain A residue 657 VAL 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 17 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 76 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 chunk 104 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.099820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.086242 restraints weight = 22614.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.089039 restraints weight = 11373.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090849 restraints weight = 6830.144| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10499 Z= 0.230 Angle : 0.648 12.090 14225 Z= 0.315 Chirality : 0.041 0.192 1632 Planarity : 0.004 0.040 1852 Dihedral : 7.222 158.130 1469 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.46 % Favored : 97.46 % Rotamer: Outliers : 3.04 % Allowed : 21.03 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1301 helix: 2.41 (0.20), residues: 684 sheet: -0.40 (0.36), residues: 195 loop : -0.61 (0.28), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.004 TRP B 436 HIS 0.004 0.001 HIS A 312 PHE 0.027 0.001 PHE B 184 TYR 0.018 0.001 TYR B 623 ARG 0.009 0.001 ARG A 194 ********************** 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 185 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 180 TYR cc_start: 0.7781 (p90) cc_final: 0.6739 (p90) REVERT: B 196 LEU cc_start: 0.7585 (OUTLIER) cc_final: 0.6778 (mp) REVERT: B 203 GLU cc_start: 0.7638 (tt0) cc_final: 0.7255 (tp30) REVERT: B 221 ASP cc_start: 0.7606 (t70) cc_final: 0.7209 (t0) REVERT: B 325 GLN cc_start: 0.8099 (mt0) cc_final: 0.7849 (mt0) REVERT: B 434 ASP cc_start: 0.7780 (m-30) cc_final: 0.7410 (m-30) REVERT: B 435 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7851 (tm-30) REVERT: B 517 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7873 (pptt) REVERT: B 538 HIS cc_start: 0.8299 (m90) cc_final: 0.7929 (m90) REVERT: B 592 LEU cc_start: 0.8960 (tp) cc_final: 0.8736 (tp) REVERT: B 622 THR cc_start: 0.8936 (m) cc_final: 0.8651 (p) REVERT: B 693 ASP cc_start: 0.7691 (t70) cc_final: 0.7393 (t0) REVERT: A 13 MET cc_start: 0.8434 (ppp) cc_final: 0.8059 (ppp) REVERT: A 41 TYR cc_start: 0.8885 (m-80) cc_final: 0.8316 (m-80) REVERT: A 43 ASP cc_start: 0.8195 (m-30) cc_final: 0.7935 (m-30) REVERT: A 129 GLN cc_start: 0.8208 (mm-40) cc_final: 0.7883 (mm110) REVERT: A 281 GLN cc_start: 0.8998 (tt0) cc_final: 0.8729 (tt0) REVERT: A 313 MET cc_start: 0.7698 (tpp) cc_final: 0.7356 (mmm) REVERT: A 404 ARG cc_start: 0.7952 (ptm160) cc_final: 0.7750 (ptm160) REVERT: A 531 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8440 (tp) REVERT: A 539 LEU cc_start: 0.9087 (tp) cc_final: 0.8859 (tp) REVERT: A 656 ARG cc_start: 0.7219 (tpm170) cc_final: 0.6855 (tpm170) REVERT: A 671 MET cc_start: 0.8178 (tpp) cc_final: 0.7948 (tpt) REVERT: A 714 ASN cc_start: 0.8417 (t0) cc_final: 0.8024 (t0) REVERT: A 794 ARG cc_start: 0.7630 (mtm180) cc_final: 0.6931 (mtm110) outliers start: 33 outliers final: 26 residues processed: 172 average time/residue: 0.2350 time to fit residues: 57.2349 Evaluate side-chains 171 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 1.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 THR Chi-restraints excluded: chain B residue 150 ILE Chi-restraints excluded: chain B residue 196 LEU Chi-restraints excluded: chain B residue 213 LEU 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 640 VAL Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 727 THR Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 86 GLN 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 141 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 258 ILE Chi-restraints excluded: chain A residue 335 THR 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 592 LEU Chi-restraints excluded: chain A residue 657 VAL 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 76 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 107 optimal weight: 0.7980 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 123 optimal weight: 8.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 746 HIS ** A 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.099593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.086012 restraints weight = 22668.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088798 restraints weight = 11431.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090628 restraints weight = 6865.727| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10499 Z= 0.233 Angle : 0.655 12.075 14225 Z= 0.317 Chirality : 0.041 0.221 1632 Planarity : 0.004 0.041 1852 Dihedral : 7.223 158.820 1469 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.77 % Favored : 97.16 % Rotamer: Outliers : 2.86 % Allowed : 21.03 % Favored : 76.11 % 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: 1.53 (0.23), residues: 1301 helix: 2.40 (0.20), residues: 684 sheet: -0.42 (0.36), residues: 195 loop : -0.59 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP A 202 HIS 0.003 0.001 HIS A 728 PHE 0.027 0.002 PHE B 184 TYR 0.018 0.001 TYR B 623 ARG 0.009 0.000 ARG A 194 =============================================================================== Job complete usr+sys time: 2799.19 seconds wall clock time: 51 minutes 9.59 seconds (3069.59 seconds total)