Starting phenix.real_space_refine on Sat Aug 23 10:03:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jun_36662/08_2025/8jun_36662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jun_36662/08_2025/8jun_36662.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jun_36662/08_2025/8jun_36662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jun_36662/08_2025/8jun_36662.map" model { file = "/net/cci-nas-00/data/ceres_data/8jun_36662/08_2025/8jun_36662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jun_36662/08_2025/8jun_36662.cif" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.101 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 2 5.49 5 S 66 5.16 5 C 7338 2.51 5 N 1764 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11098 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5496 Classifications: {'peptide': 678} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 653} Chain breaks: 1 Chain: "B" Number of atoms: 5496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 5496 Classifications: {'peptide': 678} Link IDs: {'PCIS': 3, 'PTRANS': 21, 'TRANS': 653} Chain breaks: 1 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {' ZN': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 53 Unusual residues: {' ZN': 1, 'POV': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.04, per 1000 atoms: 0.18 Number of scatterers: 11098 At special positions: 0 Unit cell: (113.42, 118.77, 121.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 66 16.00 P 2 15.00 O 1926 8.00 N 1764 7.00 C 7338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 222 " distance=2.04 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 479 " - pdb=" SG CYS A 565 " distance=2.03 Simple disulfide: pdb=" SG CYS A 485 " - pdb=" SG CYS A 782 " distance=2.03 Simple disulfide: pdb=" SG CYS B 130 " - pdb=" SG CYS B 222 " distance=2.04 Simple disulfide: pdb=" SG CYS B 212 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 479 " - pdb=" SG CYS B 565 " distance=2.03 Simple disulfide: pdb=" SG CYS B 485 " - pdb=" SG CYS B 782 " distance=2.03 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: 0.91 Conformation dependent library (CDL) restraints added in 366.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 563 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 791 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 795 " pdb=" ZN B 901 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 563 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 791 " pdb="ZN ZN B 901 " - pdb=" NE2 HIS B 795 " 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2600 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 10 sheets defined 47.6% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 251 through 253 No H-bonds generated for 'chain 'A' and resid 251 through 253' Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 302 through 332 removed outlier: 3.637A pdb=" N TYR A 306 " --> pdb=" O LYS A 302 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE A 317 " --> pdb=" O SER A 313 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 320 " --> pdb=" O ILE A 316 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR A 321 " --> pdb=" O PHE A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 470 removed outlier: 3.585A pdb=" N PHE A 445 " --> pdb=" O TYR A 441 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR A 450 " --> pdb=" O TRP A 446 " (cutoff:3.500A) Proline residue: A 458 - end of helix removed outlier: 3.558A pdb=" N LEU A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 500 removed outlier: 3.750A pdb=" N ILE A 498 " --> pdb=" O ALA A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 528 removed outlier: 3.845A pdb=" N VAL A 505 " --> pdb=" O ASN A 501 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.699A pdb=" N VAL A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 565 removed outlier: 3.782A pdb=" N ALA A 547 " --> pdb=" O GLY A 543 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N CYS A 565 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.839A pdb=" N MET A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 621 removed outlier: 3.753A pdb=" N SER A 607 " --> pdb=" O SER A 603 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE A 608 " --> pdb=" O ALA A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 625 through 647 removed outlier: 3.691A pdb=" N ILE A 631 " --> pdb=" O TRP A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 668 removed outlier: 4.631A pdb=" N PHE A 667 " --> pdb=" O ALA A 663 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 668 " --> pdb=" O ALA A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 705 removed outlier: 4.264A pdb=" N MET A 684 " --> pdb=" O TYR A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 735 Processing helix chain 'A' and resid 740 through 762 Processing helix chain 'A' and resid 771 through 777 Processing helix chain 'A' and resid 789 through 812 Processing helix chain 'A' and resid 813 through 816 Processing helix chain 'B' and resid 251 through 253 No H-bonds generated for 'chain 'B' and resid 251 through 253' Processing helix chain 'B' and resid 268 through 272 Processing helix chain 'B' and resid 302 through 332 removed outlier: 3.637A pdb=" N TYR B 306 " --> pdb=" O LYS B 302 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N PHE B 317 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 320 " --> pdb=" O ILE B 316 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR B 321 " --> pdb=" O PHE B 317 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 470 removed outlier: 3.585A pdb=" N PHE B 445 " --> pdb=" O TYR B 441 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR B 450 " --> pdb=" O TRP B 446 " (cutoff:3.500A) Proline residue: B 458 - end of helix removed outlier: 3.568A pdb=" N LEU B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL B 470 " --> pdb=" O TYR B 466 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 500 removed outlier: 3.749A pdb=" N ILE B 498 " --> pdb=" O ALA B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 528 removed outlier: 3.846A pdb=" N VAL B 505 " --> pdb=" O ASN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 530 through 535 removed outlier: 3.699A pdb=" N VAL B 534 " --> pdb=" O ASP B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 565 removed outlier: 3.783A pdb=" N ALA B 547 " --> pdb=" O GLY B 543 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS B 565 " --> pdb=" O CYS B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 576 through 592 removed outlier: 3.840A pdb=" N MET B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 621 removed outlier: 3.753A pdb=" N SER B 607 " --> pdb=" O SER B 603 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE B 608 " --> pdb=" O ALA B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 625 through 647 removed outlier: 3.691A pdb=" N ILE B 631 " --> pdb=" O TRP B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 668 removed outlier: 4.631A pdb=" N PHE B 667 " --> pdb=" O ALA B 663 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR B 668 " --> pdb=" O ALA B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 705 removed outlier: 4.264A pdb=" N MET B 684 " --> pdb=" O TYR B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 735 Processing helix chain 'B' and resid 740 through 762 Processing helix chain 'B' and resid 771 through 777 Processing helix chain 'B' and resid 789 through 812 Processing helix chain 'B' and resid 813 through 816 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 56 removed outlier: 4.426A pdb=" N VAL A 78 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70 Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113 Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181 Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192 Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 56 removed outlier: 4.427A pdb=" N VAL B 78 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 70 Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 113 Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 181 Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192 614 hydrogen bonds defined for protein. 1746 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: 1.51 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1782 1.32 - 1.44: 3257 1.44 - 1.57: 6249 1.57 - 1.69: 4 1.69 - 1.81: 102 Bond restraints: 11394 Sorted by residual: bond pdb=" C31 POV A 902 " pdb=" O31 POV A 902 " ideal model delta sigma weight residual 1.327 1.464 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C21 POV B 902 " pdb=" O21 POV B 902 " ideal model delta sigma weight residual 1.330 1.437 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C21 POV A 902 " pdb=" O21 POV A 902 " ideal model delta sigma weight residual 1.330 1.431 -0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" C31 POV B 902 " pdb=" O31 POV B 902 " ideal model delta sigma weight residual 1.327 1.423 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O12 POV A 902 " pdb=" P POV A 902 " ideal model delta sigma weight residual 1.657 1.610 0.047 2.00e-02 2.50e+03 5.56e+00 ... (remaining 11389 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.89: 15406 5.89 - 11.78: 55 11.78 - 17.66: 5 17.66 - 23.55: 3 23.55 - 29.44: 3 Bond angle restraints: 15472 Sorted by residual: angle pdb=" C12 POV A 902 " pdb=" N POV A 902 " pdb=" C15 POV A 902 " ideal model delta sigma weight residual 112.10 82.66 29.44 3.00e+00 1.11e-01 9.63e+01 angle pdb=" C14 POV A 902 " pdb=" N POV A 902 " pdb=" C15 POV A 902 " ideal model delta sigma weight residual 108.02 82.86 25.16 3.00e+00 1.11e-01 7.03e+01 angle pdb=" C14 POV B 902 " pdb=" N POV B 902 " pdb=" C15 POV B 902 " ideal model delta sigma weight residual 108.02 83.47 24.55 3.00e+00 1.11e-01 6.70e+01 angle pdb=" C12 POV B 902 " pdb=" N POV B 902 " pdb=" C15 POV B 902 " ideal model delta sigma weight residual 112.10 89.38 22.72 3.00e+00 1.11e-01 5.73e+01 angle pdb=" N LEU A 462 " pdb=" CA LEU A 462 " pdb=" C LEU A 462 " ideal model delta sigma weight residual 111.07 118.58 -7.51 1.07e+00 8.73e-01 4.93e+01 ... (remaining 15467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.43: 6136 19.43 - 38.86: 434 38.86 - 58.30: 90 58.30 - 77.73: 28 77.73 - 97.16: 6 Dihedral angle restraints: 6694 sinusoidal: 2660 harmonic: 4034 Sorted by residual: dihedral pdb=" CA ASN A 570 " pdb=" C ASN A 570 " pdb=" N PHE A 571 " pdb=" CA PHE A 571 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASN B 570 " pdb=" C ASN B 570 " pdb=" N PHE B 571 " pdb=" CA PHE B 571 " ideal model delta harmonic sigma weight residual 180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA SER B 767 " pdb=" C SER B 767 " pdb=" N TRP B 768 " pdb=" CA TRP B 768 " ideal model delta harmonic sigma weight residual 180.00 157.71 22.29 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 6691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1260 0.047 - 0.095: 361 0.095 - 0.142: 99 0.142 - 0.189: 8 0.189 - 0.237: 4 Chirality restraints: 1732 Sorted by residual: chirality pdb=" CA LEU A 462 " pdb=" N LEU A 462 " pdb=" C LEU A 462 " pdb=" CB LEU A 462 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA TYR B 668 " pdb=" N TYR B 668 " pdb=" C TYR B 668 " pdb=" CB TYR B 668 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR A 668 " pdb=" N TYR A 668 " pdb=" C TYR A 668 " pdb=" CB TYR A 668 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 1729 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 655 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.13e+00 pdb=" C ILE A 655 " 0.043 2.00e-02 2.50e+03 pdb=" O ILE A 655 " -0.016 2.00e-02 2.50e+03 pdb=" N ASP A 656 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 655 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C ILE B 655 " -0.042 2.00e-02 2.50e+03 pdb=" O ILE B 655 " 0.016 2.00e-02 2.50e+03 pdb=" N ASP B 656 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 284 " 0.010 2.00e-02 2.50e+03 2.11e-02 4.44e+00 pdb=" C THR B 284 " -0.036 2.00e-02 2.50e+03 pdb=" O THR B 284 " 0.014 2.00e-02 2.50e+03 pdb=" N TRP B 285 " 0.012 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 54 2.57 - 3.15: 9023 3.15 - 3.73: 17013 3.73 - 4.32: 25671 4.32 - 4.90: 41145 Nonbonded interactions: 92906 Sorted by model distance: nonbonded pdb=" C11 POV B 902 " pdb=" C15 POV B 902 " model vdw 1.983 3.088 nonbonded pdb=" C11 POV A 902 " pdb=" C15 POV A 902 " model vdw 2.050 3.088 nonbonded pdb=" OD1 ASP A 574 " pdb="ZN ZN A 901 " model vdw 2.070 2.230 nonbonded pdb=" OD1 ASP B 574 " pdb="ZN ZN B 901 " model vdw 2.071 2.230 nonbonded pdb=" O GLU B 124 " pdb=" OG SER B 184 " model vdw 2.181 3.040 ... (remaining 92901 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 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 : 0.009 0.269 11408 Z= 0.350 Angle : 1.000 29.441 15488 Z= 0.475 Chirality : 0.048 0.237 1732 Planarity : 0.004 0.038 1920 Dihedral : 14.892 97.160 4070 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.69 (0.21), residues: 1348 helix: -0.70 (0.20), residues: 560 sheet: 0.72 (0.28), residues: 278 loop : -2.66 (0.24), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 821 TYR 0.026 0.002 TYR A 680 PHE 0.018 0.002 PHE B 697 TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS A 487 Details of bonding type rmsd covalent geometry : bond 0.00690 (11394) covalent geometry : angle 1.00025 (15472) SS BOND : bond 0.00390 ( 8) SS BOND : angle 0.70432 ( 16) hydrogen bonds : bond 0.14550 ( 614) hydrogen bonds : angle 6.31842 ( 1746) metal coordination : bond 0.23170 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6293 (mmm-85) cc_final: 0.5645 (ttm170) REVERT: A 118 ARG cc_start: 0.7337 (ttm110) cc_final: 0.7120 (ttt90) REVERT: A 145 ILE cc_start: 0.9085 (mt) cc_final: 0.8876 (mp) REVERT: A 641 LEU cc_start: 0.7522 (tp) cc_final: 0.7157 (mt) REVERT: B 44 ARG cc_start: 0.6878 (mmm-85) cc_final: 0.6304 (tmt170) REVERT: B 101 LYS cc_start: 0.8885 (mtmm) cc_final: 0.8648 (mtpp) REVERT: B 115 LEU cc_start: 0.8438 (mt) cc_final: 0.8232 (mt) REVERT: B 152 MET cc_start: 0.8624 (mtt) cc_final: 0.8349 (mtt) REVERT: B 222 CYS cc_start: 0.7374 (m) cc_final: 0.6953 (m) REVERT: B 240 MET cc_start: 0.9162 (ttt) cc_final: 0.8885 (ttt) REVERT: B 617 LEU cc_start: 0.7840 (mt) cc_final: 0.7594 (mm) REVERT: B 623 LYS cc_start: 0.7764 (mptt) cc_final: 0.7381 (mmtm) REVERT: B 652 ARG cc_start: 0.6905 (mmt180) cc_final: 0.5815 (mtt180) REVERT: B 783 ILE cc_start: 0.8371 (tt) cc_final: 0.8164 (pt) outliers start: 0 outliers final: 1 residues processed: 193 average time/residue: 0.4563 time to fit residues: 95.8690 Evaluate side-chains 144 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 143 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 625 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 504 HIS A 591 GLN A 763 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 117 GLN B 142 GLN B 185 GLN B 504 HIS B 541 HIS B 591 GLN B 691 ASN B 694 ASN B 763 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.157513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.105504 restraints weight = 12157.331| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.28 r_work: 0.3201 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11408 Z= 0.137 Angle : 0.537 7.520 15488 Z= 0.289 Chirality : 0.043 0.137 1732 Planarity : 0.003 0.033 1920 Dihedral : 9.730 91.572 1572 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.49 % Allowed : 8.61 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.22), residues: 1348 helix: 0.78 (0.21), residues: 594 sheet: 0.99 (0.28), residues: 282 loop : -2.13 (0.26), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 44 TYR 0.017 0.002 TYR B 680 PHE 0.012 0.001 PHE B 445 TRP 0.009 0.001 TRP B 629 HIS 0.005 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00300 (11394) covalent geometry : angle 0.53663 (15472) SS BOND : bond 0.00084 ( 8) SS BOND : angle 0.69678 ( 16) hydrogen bonds : bond 0.04888 ( 614) hydrogen bonds : angle 4.60787 ( 1746) metal coordination : bond 0.00620 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6490 (mmm-85) cc_final: 0.5555 (ttm170) REVERT: A 118 ARG cc_start: 0.7775 (ttm110) cc_final: 0.7090 (ttt90) REVERT: A 145 ILE cc_start: 0.9076 (mt) cc_final: 0.8821 (mp) REVERT: A 536 TYR cc_start: 0.7073 (m-80) cc_final: 0.6621 (m-80) REVERT: A 650 MET cc_start: 0.7003 (mtt) cc_final: 0.6562 (mtt) REVERT: B 44 ARG cc_start: 0.6814 (mmm-85) cc_final: 0.6119 (tmt170) REVERT: B 83 ASN cc_start: 0.7774 (p0) cc_final: 0.7472 (p0) REVERT: B 115 LEU cc_start: 0.8345 (mt) cc_final: 0.8088 (mt) REVERT: B 143 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.7857 (mm110) REVERT: B 195 LYS cc_start: 0.8476 (mppt) cc_final: 0.8157 (tppt) REVERT: B 207 GLU cc_start: 0.7616 (mp0) cc_final: 0.7307 (mp0) REVERT: B 523 ARG cc_start: 0.7211 (ttp-170) cc_final: 0.6990 (mtp180) REVERT: B 536 TYR cc_start: 0.7747 (m-80) cc_final: 0.7471 (m-80) REVERT: B 617 LEU cc_start: 0.7760 (mt) cc_final: 0.7503 (mm) REVERT: B 652 ARG cc_start: 0.5877 (mmt180) cc_final: 0.4709 (mtt180) REVERT: B 783 ILE cc_start: 0.8538 (tt) cc_final: 0.8304 (pt) outliers start: 18 outliers final: 4 residues processed: 163 average time/residue: 0.4555 time to fit residues: 81.2167 Evaluate side-chains 137 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 132 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 449 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 118 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 67 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 117 GLN B 142 GLN B 497 ASN B 541 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.154601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.102372 restraints weight = 12242.379| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.30 r_work: 0.3159 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11408 Z= 0.177 Angle : 0.557 6.875 15488 Z= 0.298 Chirality : 0.044 0.154 1732 Planarity : 0.003 0.031 1920 Dihedral : 9.041 85.545 1570 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.90 % Allowed : 10.10 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.23), residues: 1348 helix: 1.13 (0.21), residues: 606 sheet: 1.25 (0.28), residues: 278 loop : -1.91 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 820 TYR 0.015 0.002 TYR B 680 PHE 0.014 0.002 PHE B 632 TRP 0.011 0.001 TRP B 629 HIS 0.005 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00409 (11394) covalent geometry : angle 0.55380 (15472) SS BOND : bond 0.00187 ( 8) SS BOND : angle 1.87579 ( 16) hydrogen bonds : bond 0.04973 ( 614) hydrogen bonds : angle 4.48947 ( 1746) metal coordination : bond 0.00815 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6721 (mmm-85) cc_final: 0.6106 (ttm170) REVERT: A 63 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.7865 (tp) REVERT: A 118 ARG cc_start: 0.7824 (ttm110) cc_final: 0.7106 (ttt90) REVERT: A 143 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: A 145 ILE cc_start: 0.9048 (mt) cc_final: 0.8787 (mp) REVERT: A 536 TYR cc_start: 0.7183 (m-80) cc_final: 0.6566 (m-80) REVERT: A 554 MET cc_start: 0.8288 (tpp) cc_final: 0.7981 (mmt) REVERT: A 613 MET cc_start: 0.7946 (tpt) cc_final: 0.7618 (mmm) REVERT: A 650 MET cc_start: 0.7240 (mtt) cc_final: 0.6877 (mtp) REVERT: A 691 ASN cc_start: 0.7666 (m-40) cc_final: 0.7437 (t0) REVERT: B 44 ARG cc_start: 0.6922 (mmm-85) cc_final: 0.6445 (tmt90) REVERT: B 63 ILE cc_start: 0.8722 (mt) cc_final: 0.8455 (mm) REVERT: B 83 ASN cc_start: 0.8018 (p0) cc_final: 0.7664 (p0) REVERT: B 115 LEU cc_start: 0.8405 (mt) cc_final: 0.8168 (mt) REVERT: B 195 LYS cc_start: 0.8572 (mppt) cc_final: 0.8301 (tppt) REVERT: B 207 GLU cc_start: 0.7535 (mp0) cc_final: 0.7153 (mp0) REVERT: B 221 MET cc_start: 0.8044 (mtp) cc_final: 0.7376 (mpt) REVERT: B 446 TRP cc_start: 0.6094 (OUTLIER) cc_final: 0.5265 (m100) REVERT: B 536 TYR cc_start: 0.7655 (m-80) cc_final: 0.7255 (m-80) REVERT: B 621 PHE cc_start: 0.8542 (m-80) cc_final: 0.8244 (m-80) REVERT: B 623 LYS cc_start: 0.7276 (mptt) cc_final: 0.6986 (mmtm) REVERT: B 650 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.6318 (mtt) REVERT: B 652 ARG cc_start: 0.6438 (mmt180) cc_final: 0.5192 (mtt180) outliers start: 23 outliers final: 9 residues processed: 159 average time/residue: 0.4534 time to fit residues: 78.7704 Evaluate side-chains 150 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 641 LEU Chi-restraints excluded: chain B residue 650 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 127 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 133 optimal weight: 0.7980 chunk 120 optimal weight: 20.0000 chunk 49 optimal weight: 10.0000 chunk 109 optimal weight: 0.0060 chunk 74 optimal weight: 0.2980 chunk 58 optimal weight: 5.9990 chunk 6 optimal weight: 0.5980 chunk 70 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 142 GLN B 447 ASN B 779 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.158091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.106595 restraints weight = 12255.354| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.31 r_work: 0.3219 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11408 Z= 0.106 Angle : 0.483 5.816 15488 Z= 0.257 Chirality : 0.042 0.141 1732 Planarity : 0.003 0.029 1920 Dihedral : 8.257 80.323 1570 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.82 % Allowed : 11.34 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.23), residues: 1348 helix: 1.52 (0.21), residues: 602 sheet: 1.36 (0.29), residues: 282 loop : -1.90 (0.27), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 821 TYR 0.011 0.001 TYR B 680 PHE 0.009 0.001 PHE B 258 TRP 0.008 0.001 TRP B 629 HIS 0.005 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00228 (11394) covalent geometry : angle 0.48032 (15472) SS BOND : bond 0.00165 ( 8) SS BOND : angle 1.53783 ( 16) hydrogen bonds : bond 0.04011 ( 614) hydrogen bonds : angle 4.10384 ( 1746) metal coordination : bond 0.00528 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 153 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6888 (mmm-85) cc_final: 0.6433 (ttm170) REVERT: A 63 ILE cc_start: 0.8415 (mm) cc_final: 0.7806 (tp) REVERT: A 118 ARG cc_start: 0.7858 (ttm110) cc_final: 0.7157 (ttt90) REVERT: A 143 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8130 (mt0) REVERT: A 145 ILE cc_start: 0.9025 (mt) cc_final: 0.8751 (mp) REVERT: A 536 TYR cc_start: 0.7180 (m-80) cc_final: 0.6617 (m-80) REVERT: A 540 LYS cc_start: 0.8156 (mttm) cc_final: 0.7850 (mmtt) REVERT: A 554 MET cc_start: 0.8202 (tpp) cc_final: 0.7932 (mmt) REVERT: A 613 MET cc_start: 0.7904 (tpt) cc_final: 0.7523 (mmm) REVERT: B 44 ARG cc_start: 0.6825 (mmm-85) cc_final: 0.6543 (tmt90) REVERT: B 63 ILE cc_start: 0.8710 (mt) cc_final: 0.8453 (mm) REVERT: B 115 LEU cc_start: 0.8512 (mt) cc_final: 0.8280 (mt) REVERT: B 121 ASN cc_start: 0.8927 (p0) cc_final: 0.8416 (p0) REVERT: B 195 LYS cc_start: 0.8582 (mppt) cc_final: 0.8338 (tppt) REVERT: B 221 MET cc_start: 0.7795 (mtp) cc_final: 0.7314 (mpm) REVERT: B 536 TYR cc_start: 0.7486 (m-80) cc_final: 0.7163 (m-80) REVERT: B 617 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7527 (mm) REVERT: B 621 PHE cc_start: 0.8487 (m-80) cc_final: 0.8111 (m-80) REVERT: B 650 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.6483 (mtt) REVERT: B 652 ARG cc_start: 0.6373 (mmt180) cc_final: 0.5134 (mtm110) outliers start: 22 outliers final: 6 residues processed: 163 average time/residue: 0.4374 time to fit residues: 78.1300 Evaluate side-chains 148 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 18 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 59 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN ** A 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 497 ASN ** A 691 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 113 GLN B 779 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.150312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.100578 restraints weight = 12385.398| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.19 r_work: 0.3120 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 11408 Z= 0.294 Angle : 0.643 7.520 15488 Z= 0.341 Chirality : 0.048 0.214 1732 Planarity : 0.004 0.054 1920 Dihedral : 8.910 88.939 1570 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.90 % Allowed : 12.00 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.39 (0.23), residues: 1348 helix: 1.12 (0.21), residues: 610 sheet: 1.49 (0.29), residues: 278 loop : -1.77 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 821 TYR 0.024 0.002 TYR A 724 PHE 0.019 0.002 PHE A 632 TRP 0.018 0.002 TRP B 629 HIS 0.004 0.001 HIS B 795 Details of bonding type rmsd covalent geometry : bond 0.00698 (11394) covalent geometry : angle 0.64116 (15472) SS BOND : bond 0.00343 ( 8) SS BOND : angle 1.55561 ( 16) hydrogen bonds : bond 0.05666 ( 614) hydrogen bonds : angle 4.50421 ( 1746) metal coordination : bond 0.01134 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6592 (mmm-85) cc_final: 0.6158 (ttp-170) REVERT: A 63 ILE cc_start: 0.8579 (OUTLIER) cc_final: 0.7926 (tp) REVERT: A 90 ASN cc_start: 0.8072 (m-40) cc_final: 0.7790 (m-40) REVERT: A 118 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7251 (ttt90) REVERT: A 143 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.8152 (mt0) REVERT: A 145 ILE cc_start: 0.9073 (mt) cc_final: 0.8792 (mp) REVERT: A 540 LYS cc_start: 0.8360 (mttm) cc_final: 0.8000 (mmtt) REVERT: A 554 MET cc_start: 0.8317 (tpp) cc_final: 0.7995 (mmt) REVERT: A 602 TYR cc_start: 0.4507 (OUTLIER) cc_final: 0.3040 (m-80) REVERT: A 707 ARG cc_start: 0.8051 (tpt-90) cc_final: 0.7521 (mtp180) REVERT: B 44 ARG cc_start: 0.7096 (mmm-85) cc_final: 0.6580 (tmt90) REVERT: B 63 ILE cc_start: 0.8753 (mt) cc_final: 0.8434 (mm) REVERT: B 115 LEU cc_start: 0.8399 (mt) cc_final: 0.8194 (mt) REVERT: B 446 TRP cc_start: 0.6445 (OUTLIER) cc_final: 0.5457 (m100) REVERT: B 536 TYR cc_start: 0.7670 (m-80) cc_final: 0.7352 (m-80) REVERT: B 617 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7501 (mt) REVERT: B 621 PHE cc_start: 0.8545 (m-80) cc_final: 0.8182 (m-80) REVERT: B 650 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6404 (mtt) REVERT: B 652 ARG cc_start: 0.6694 (mmt180) cc_final: 0.5395 (mtm110) outliers start: 23 outliers final: 11 residues processed: 162 average time/residue: 0.4461 time to fit residues: 79.1186 Evaluate side-chains 165 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 650 MET Chi-restraints excluded: chain B residue 692 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 90 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 109 optimal weight: 0.6980 chunk 67 optimal weight: 8.9990 chunk 88 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN A 691 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 779 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.154668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.105293 restraints weight = 12410.922| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.22 r_work: 0.3189 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11408 Z= 0.117 Angle : 0.502 6.774 15488 Z= 0.267 Chirality : 0.042 0.140 1732 Planarity : 0.003 0.032 1920 Dihedral : 8.161 81.407 1570 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.90 % Allowed : 12.67 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.65 (0.23), residues: 1348 helix: 1.46 (0.21), residues: 610 sheet: 1.46 (0.29), residues: 282 loop : -1.75 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 821 TYR 0.014 0.001 TYR A 210 PHE 0.010 0.001 PHE B 632 TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00254 (11394) covalent geometry : angle 0.50050 (15472) SS BOND : bond 0.00142 ( 8) SS BOND : angle 1.12936 ( 16) hydrogen bonds : bond 0.04259 ( 614) hydrogen bonds : angle 4.17094 ( 1746) metal coordination : bond 0.00565 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6672 (mmm-85) cc_final: 0.6439 (ttp-170) REVERT: A 63 ILE cc_start: 0.8388 (mm) cc_final: 0.7780 (tp) REVERT: A 90 ASN cc_start: 0.7947 (m-40) cc_final: 0.7654 (m-40) REVERT: A 118 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7230 (ttt90) REVERT: A 143 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8146 (mt0) REVERT: A 145 ILE cc_start: 0.9025 (mt) cc_final: 0.8733 (mp) REVERT: A 536 TYR cc_start: 0.7212 (m-80) cc_final: 0.6649 (m-80) REVERT: A 540 LYS cc_start: 0.8269 (mttm) cc_final: 0.7937 (mmtt) REVERT: A 554 MET cc_start: 0.8197 (tpp) cc_final: 0.7934 (mmt) REVERT: A 602 TYR cc_start: 0.4412 (OUTLIER) cc_final: 0.3313 (m-80) REVERT: A 613 MET cc_start: 0.7951 (tpt) cc_final: 0.7606 (mmm) REVERT: A 700 PHE cc_start: 0.6809 (m-10) cc_final: 0.6593 (m-80) REVERT: A 707 ARG cc_start: 0.7895 (tpt-90) cc_final: 0.7372 (mtp180) REVERT: B 44 ARG cc_start: 0.6995 (mmm-85) cc_final: 0.6604 (tmt90) REVERT: B 63 ILE cc_start: 0.8647 (mt) cc_final: 0.8352 (mm) REVERT: B 71 GLN cc_start: 0.7838 (mm-40) cc_final: 0.7462 (mp-120) REVERT: B 115 LEU cc_start: 0.8391 (mt) cc_final: 0.8175 (mt) REVERT: B 195 LYS cc_start: 0.8758 (tppt) cc_final: 0.8378 (mppt) REVERT: B 446 TRP cc_start: 0.6459 (OUTLIER) cc_final: 0.5485 (m100) REVERT: B 536 TYR cc_start: 0.7491 (m-80) cc_final: 0.7265 (m-80) REVERT: B 617 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7473 (mt) REVERT: B 621 PHE cc_start: 0.8579 (m-80) cc_final: 0.8246 (m-80) REVERT: B 650 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6468 (mtt) REVERT: B 652 ARG cc_start: 0.6488 (mmt180) cc_final: 0.5188 (mtm110) outliers start: 23 outliers final: 11 residues processed: 160 average time/residue: 0.4359 time to fit residues: 76.4440 Evaluate side-chains 155 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 617 LEU Chi-restraints excluded: chain B residue 640 SER Chi-restraints excluded: chain B residue 650 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 45 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 88 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 691 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.152642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103074 restraints weight = 12294.281| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 2.21 r_work: 0.3153 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 11408 Z= 0.190 Angle : 0.567 10.195 15488 Z= 0.300 Chirality : 0.044 0.169 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.264 83.378 1570 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.15 % Allowed : 12.58 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.23), residues: 1348 helix: 1.48 (0.21), residues: 604 sheet: 1.49 (0.28), residues: 286 loop : -1.70 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 821 TYR 0.015 0.002 TYR A 188 PHE 0.015 0.002 PHE B 632 TRP 0.014 0.001 TRP B 629 HIS 0.003 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00448 (11394) covalent geometry : angle 0.56219 (15472) SS BOND : bond 0.00194 ( 8) SS BOND : angle 2.31433 ( 16) hydrogen bonds : bond 0.04819 ( 614) hydrogen bonds : angle 4.31214 ( 1746) metal coordination : bond 0.00819 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6675 (mmm-85) cc_final: 0.6428 (ttp-170) REVERT: A 63 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.7789 (tp) REVERT: A 90 ASN cc_start: 0.7996 (m-40) cc_final: 0.7720 (m-40) REVERT: A 118 ARG cc_start: 0.7905 (ttm110) cc_final: 0.7254 (ttt90) REVERT: A 143 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: A 145 ILE cc_start: 0.9043 (mt) cc_final: 0.8768 (mp) REVERT: A 536 TYR cc_start: 0.7283 (m-80) cc_final: 0.6754 (m-80) REVERT: A 540 LYS cc_start: 0.8293 (mttm) cc_final: 0.7960 (mmtt) REVERT: A 554 MET cc_start: 0.8284 (tpp) cc_final: 0.7974 (mmt) REVERT: A 602 TYR cc_start: 0.4423 (OUTLIER) cc_final: 0.3031 (m-80) REVERT: A 613 MET cc_start: 0.7992 (tpt) cc_final: 0.7581 (mmm) REVERT: A 700 PHE cc_start: 0.6816 (m-10) cc_final: 0.6602 (m-80) REVERT: A 707 ARG cc_start: 0.7951 (tpt-90) cc_final: 0.7379 (mtp180) REVERT: B 44 ARG cc_start: 0.7020 (mmm-85) cc_final: 0.6692 (tmt90) REVERT: B 63 ILE cc_start: 0.8712 (mt) cc_final: 0.8410 (mm) REVERT: B 115 LEU cc_start: 0.8392 (mt) cc_final: 0.8179 (mt) REVERT: B 207 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8036 (mp0) REVERT: B 446 TRP cc_start: 0.6428 (OUTLIER) cc_final: 0.5483 (m100) REVERT: B 478 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8422 (mt) REVERT: B 536 TYR cc_start: 0.7511 (m-80) cc_final: 0.7229 (m-80) REVERT: B 621 PHE cc_start: 0.8599 (m-80) cc_final: 0.8277 (m-80) REVERT: B 650 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6405 (mtt) REVERT: B 652 ARG cc_start: 0.6691 (mmt180) cc_final: 0.5298 (mtm110) outliers start: 26 outliers final: 13 residues processed: 158 average time/residue: 0.4521 time to fit residues: 78.2805 Evaluate side-chains 161 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 641 LEU Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 207 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 650 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 76 optimal weight: 6.9990 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 116 optimal weight: 8.9990 chunk 126 optimal weight: 0.0030 chunk 33 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 130 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN A 764 ASN B 71 GLN B 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.157391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.105914 restraints weight = 12245.690| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.32 r_work: 0.3210 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11408 Z= 0.109 Angle : 0.493 11.209 15488 Z= 0.260 Chirality : 0.042 0.150 1732 Planarity : 0.003 0.032 1920 Dihedral : 7.685 78.252 1570 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.07 % Allowed : 13.16 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.23), residues: 1348 helix: 1.77 (0.21), residues: 598 sheet: 1.55 (0.29), residues: 282 loop : -1.63 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 821 TYR 0.012 0.001 TYR A 210 PHE 0.011 0.001 PHE B 632 TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00237 (11394) covalent geometry : angle 0.49179 (15472) SS BOND : bond 0.00122 ( 8) SS BOND : angle 1.09242 ( 16) hydrogen bonds : bond 0.03963 ( 614) hydrogen bonds : angle 4.07663 ( 1746) metal coordination : bond 0.00539 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8297 (mm) cc_final: 0.7701 (tp) REVERT: A 90 ASN cc_start: 0.7939 (m-40) cc_final: 0.7662 (m-40) REVERT: A 118 ARG cc_start: 0.7866 (ttm110) cc_final: 0.7281 (ttt90) REVERT: A 143 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: A 145 ILE cc_start: 0.9024 (mt) cc_final: 0.8739 (mp) REVERT: A 536 TYR cc_start: 0.7224 (m-80) cc_final: 0.6673 (m-80) REVERT: A 540 LYS cc_start: 0.8229 (mttm) cc_final: 0.7962 (mmtt) REVERT: A 554 MET cc_start: 0.8096 (tpp) cc_final: 0.7892 (mmt) REVERT: A 602 TYR cc_start: 0.4370 (OUTLIER) cc_final: 0.3284 (m-80) REVERT: A 613 MET cc_start: 0.8050 (tpt) cc_final: 0.7670 (mmm) REVERT: A 707 ARG cc_start: 0.7867 (tpt-90) cc_final: 0.7352 (mtp180) REVERT: B 44 ARG cc_start: 0.6944 (mmm-85) cc_final: 0.6579 (tmt90) REVERT: B 63 ILE cc_start: 0.8616 (mt) cc_final: 0.8337 (mm) REVERT: B 71 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7498 (mp-120) REVERT: B 115 LEU cc_start: 0.8500 (mt) cc_final: 0.8250 (mt) REVERT: B 121 ASN cc_start: 0.8906 (p0) cc_final: 0.8415 (p0) REVERT: B 195 LYS cc_start: 0.8731 (tppt) cc_final: 0.8364 (mppt) REVERT: B 446 TRP cc_start: 0.6504 (OUTLIER) cc_final: 0.5493 (m100) REVERT: B 536 TYR cc_start: 0.7345 (m-80) cc_final: 0.7139 (m-80) REVERT: B 621 PHE cc_start: 0.8544 (m-80) cc_final: 0.8276 (m-80) REVERT: B 652 ARG cc_start: 0.6531 (mmt180) cc_final: 0.5196 (mtm110) outliers start: 25 outliers final: 10 residues processed: 161 average time/residue: 0.5123 time to fit residues: 90.8420 Evaluate side-chains 150 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 79 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 20.0000 chunk 108 optimal weight: 0.0980 chunk 83 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN B 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.153297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.101258 restraints weight = 12174.162| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.30 r_work: 0.3141 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 11408 Z= 0.211 Angle : 0.584 11.355 15488 Z= 0.306 Chirality : 0.045 0.177 1732 Planarity : 0.004 0.042 1920 Dihedral : 8.027 81.836 1570 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.57 % Allowed : 13.49 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.23), residues: 1348 helix: 1.57 (0.21), residues: 604 sheet: 1.58 (0.28), residues: 286 loop : -1.60 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 705 TYR 0.017 0.002 TYR A 724 PHE 0.015 0.002 PHE A 632 TRP 0.015 0.002 TRP B 629 HIS 0.003 0.001 HIS B 229 Details of bonding type rmsd covalent geometry : bond 0.00498 (11394) covalent geometry : angle 0.57854 (15472) SS BOND : bond 0.00209 ( 8) SS BOND : angle 2.48985 ( 16) hydrogen bonds : bond 0.04916 ( 614) hydrogen bonds : angle 4.27719 ( 1746) metal coordination : bond 0.00893 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 142 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8420 (OUTLIER) cc_final: 0.7816 (tp) REVERT: A 90 ASN cc_start: 0.8087 (m-40) cc_final: 0.7770 (m-40) REVERT: A 118 ARG cc_start: 0.7895 (ttm110) cc_final: 0.7200 (ttt90) REVERT: A 143 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8114 (mt0) REVERT: A 145 ILE cc_start: 0.9041 (mt) cc_final: 0.8764 (mp) REVERT: A 536 TYR cc_start: 0.7304 (m-80) cc_final: 0.6707 (m-80) REVERT: A 540 LYS cc_start: 0.8300 (mttm) cc_final: 0.8010 (mmmt) REVERT: A 554 MET cc_start: 0.8189 (tpp) cc_final: 0.7894 (mmt) REVERT: A 602 TYR cc_start: 0.4353 (OUTLIER) cc_final: 0.3115 (m-80) REVERT: A 613 MET cc_start: 0.8020 (tpt) cc_final: 0.7594 (mmm) REVERT: A 707 ARG cc_start: 0.7983 (tpt-90) cc_final: 0.7497 (mtp180) REVERT: B 44 ARG cc_start: 0.7020 (mmm-85) cc_final: 0.6592 (tmt90) REVERT: B 63 ILE cc_start: 0.8707 (mt) cc_final: 0.8402 (mm) REVERT: B 115 LEU cc_start: 0.8361 (mt) cc_final: 0.8156 (mt) REVERT: B 446 TRP cc_start: 0.6562 (OUTLIER) cc_final: 0.5547 (m100) REVERT: B 478 ILE cc_start: 0.8774 (OUTLIER) cc_final: 0.8423 (mt) REVERT: B 536 TYR cc_start: 0.7455 (m-80) cc_final: 0.7171 (m-80) REVERT: B 621 PHE cc_start: 0.8609 (m-80) cc_final: 0.8304 (m-80) REVERT: B 635 ILE cc_start: 0.8282 (pt) cc_final: 0.8054 (mp) REVERT: B 652 ARG cc_start: 0.6564 (mmt180) cc_final: 0.6131 (mpt180) outliers start: 19 outliers final: 10 residues processed: 155 average time/residue: 0.5559 time to fit residues: 94.2366 Evaluate side-chains 153 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 138 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 478 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 130 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 63 optimal weight: 0.4980 chunk 64 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 32 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 143 GLN A 691 ASN B 71 GLN B 158 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.156608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104905 restraints weight = 12299.920| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.33 r_work: 0.3195 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11408 Z= 0.116 Angle : 0.508 10.454 15488 Z= 0.267 Chirality : 0.042 0.178 1732 Planarity : 0.003 0.033 1920 Dihedral : 7.590 77.682 1570 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.16 % Allowed : 13.99 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.23), residues: 1348 helix: 1.71 (0.21), residues: 604 sheet: 1.58 (0.29), residues: 282 loop : -1.50 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 821 TYR 0.012 0.001 TYR A 188 PHE 0.011 0.001 PHE B 632 TRP 0.006 0.001 TRP A 629 HIS 0.005 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00252 (11394) covalent geometry : angle 0.50613 (15472) SS BOND : bond 0.00167 ( 8) SS BOND : angle 1.28462 ( 16) hydrogen bonds : bond 0.04102 ( 614) hydrogen bonds : angle 4.08271 ( 1746) metal coordination : bond 0.00566 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: A 90 ASN cc_start: 0.8063 (m-40) cc_final: 0.7751 (m-40) REVERT: A 118 ARG cc_start: 0.7875 (ttm110) cc_final: 0.7232 (ttt90) REVERT: A 145 ILE cc_start: 0.9041 (mt) cc_final: 0.8762 (mp) REVERT: A 536 TYR cc_start: 0.7151 (m-80) cc_final: 0.6614 (m-80) REVERT: A 540 LYS cc_start: 0.8229 (mttm) cc_final: 0.7916 (mmtt) REVERT: A 554 MET cc_start: 0.8082 (tpp) cc_final: 0.7874 (mmt) REVERT: A 602 TYR cc_start: 0.4422 (OUTLIER) cc_final: 0.3300 (m-80) REVERT: A 613 MET cc_start: 0.8045 (tpt) cc_final: 0.7640 (mmm) REVERT: A 707 ARG cc_start: 0.7899 (tpt-90) cc_final: 0.7391 (mtp180) REVERT: B 44 ARG cc_start: 0.7006 (mmm-85) cc_final: 0.6610 (tmt90) REVERT: B 63 ILE cc_start: 0.8609 (mt) cc_final: 0.8322 (mm) REVERT: B 71 GLN cc_start: 0.7909 (mm-40) cc_final: 0.7521 (mp-120) REVERT: B 115 LEU cc_start: 0.8485 (mt) cc_final: 0.8235 (mt) REVERT: B 118 ARG cc_start: 0.7759 (ttm-80) cc_final: 0.7259 (mtp180) REVERT: B 121 ASN cc_start: 0.8959 (p0) cc_final: 0.8438 (p0) REVERT: B 446 TRP cc_start: 0.6610 (OUTLIER) cc_final: 0.5591 (m100) REVERT: B 478 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8365 (mt) REVERT: B 523 ARG cc_start: 0.6328 (mtp180) cc_final: 0.5037 (mtt90) REVERT: B 536 TYR cc_start: 0.7318 (m-80) cc_final: 0.7115 (m-80) REVERT: B 621 PHE cc_start: 0.8579 (m-80) cc_final: 0.8209 (m-80) REVERT: B 652 ARG cc_start: 0.6306 (mmt180) cc_final: 0.5050 (mtm110) outliers start: 14 outliers final: 10 residues processed: 149 average time/residue: 0.5439 time to fit residues: 88.6506 Evaluate side-chains 149 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 136 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain B residue 76 THR Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 478 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 84 optimal weight: 2.9990 chunk 39 optimal weight: 0.2980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 130 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 691 ASN B 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.156361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.105105 restraints weight = 12333.070| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.30 r_work: 0.3196 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11408 Z= 0.121 Angle : 0.517 9.258 15488 Z= 0.272 Chirality : 0.043 0.179 1732 Planarity : 0.003 0.033 1920 Dihedral : 7.514 76.271 1570 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.08 % Allowed : 13.82 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.23), residues: 1348 helix: 1.77 (0.21), residues: 604 sheet: 1.59 (0.28), residues: 286 loop : -1.41 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 707 TYR 0.013 0.001 TYR A 188 PHE 0.011 0.001 PHE B 632 TRP 0.007 0.001 TRP A 629 HIS 0.006 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00267 (11394) covalent geometry : angle 0.51369 (15472) SS BOND : bond 0.00141 ( 8) SS BOND : angle 1.99238 ( 16) hydrogen bonds : bond 0.04163 ( 614) hydrogen bonds : angle 4.06782 ( 1746) metal coordination : bond 0.00576 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4832.10 seconds wall clock time: 82 minutes 49.50 seconds (4969.50 seconds total)