Starting phenix.real_space_refine on Tue Jul 29 12:27:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jun_36662/07_2025/8jun_36662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jun_36662/07_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_36662/07_2025/8jun_36662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jun_36662/07_2025/8jun_36662.map" model { file = "/net/cci-nas-00/data/ceres_data/8jun_36662/07_2025/8jun_36662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jun_36662/07_2025/8jun_36662.cif" } resolution = 2.38 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.98, per 1000 atoms: 0.63 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: 2.64 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.29 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: 3.36 Time building geometry restraints manager: 3.16 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: 0.06 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: 1.420 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: 0.020 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 29.460 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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:12.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.100 ------------------------------------------------------------------------------- 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 (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: -1.69 (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 TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS A 487 PHE 0.018 0.002 PHE B 697 TYR 0.026 0.002 TYR A 680 ARG 0.008 0.001 ARG A 821 Details of bonding type rmsd hydrogen bonds : bond 0.14550 ( 614) hydrogen bonds : angle 6.31842 ( 1746) metal coordination : bond 0.23170 ( 6) SS BOND : bond 0.00390 ( 8) SS BOND : angle 0.70432 ( 16) covalent geometry : bond 0.00690 (11394) covalent geometry : angle 1.00025 (15472) *********************** 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 : 1.162 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: 0.7165 (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: 1.1792 time to fit residues: 248.0692 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 : 1.389 ------------------------------------------------------------------------------- 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 113 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 68 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 105 optimal weight: 8.9990 chunk 40 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 0.7980 chunk 121 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.155728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.103565 restraints weight = 12061.935| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.27 r_work: 0.3174 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11408 Z= 0.164 Angle : 0.558 7.444 15488 Z= 0.300 Chirality : 0.044 0.146 1732 Planarity : 0.004 0.034 1920 Dihedral : 9.691 91.396 1572 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.49 % Allowed : 8.94 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.22), residues: 1348 helix: 0.67 (0.21), residues: 602 sheet: 1.09 (0.28), residues: 278 loop : -2.09 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.005 0.001 HIS B 594 PHE 0.013 0.001 PHE B 445 TYR 0.016 0.002 TYR A 680 ARG 0.003 0.000 ARG B 821 Details of bonding type rmsd hydrogen bonds : bond 0.05013 ( 614) hydrogen bonds : angle 4.64879 ( 1746) metal coordination : bond 0.00858 ( 6) SS BOND : bond 0.00130 ( 8) SS BOND : angle 0.81403 ( 16) covalent geometry : bond 0.00371 (11394) covalent geometry : angle 0.55767 (15472) *********************** 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 : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6522 (mmm-85) cc_final: 0.5620 (ttp-170) REVERT: A 118 ARG cc_start: 0.7811 (ttm110) cc_final: 0.7143 (ttt90) REVERT: A 145 ILE cc_start: 0.9084 (mt) cc_final: 0.8819 (mp) REVERT: A 536 TYR cc_start: 0.7138 (m-80) cc_final: 0.6569 (m-80) REVERT: A 650 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6722 (mtt) REVERT: B 44 ARG cc_start: 0.6885 (mmm-85) cc_final: 0.6173 (tmt170) REVERT: B 83 ASN cc_start: 0.7841 (p0) cc_final: 0.7541 (p0) REVERT: B 115 LEU cc_start: 0.8389 (mt) cc_final: 0.8137 (mt) REVERT: B 195 LYS cc_start: 0.8570 (mppt) cc_final: 0.8285 (tppt) REVERT: B 207 GLU cc_start: 0.7615 (mp0) cc_final: 0.7235 (mp0) REVERT: B 536 TYR cc_start: 0.7732 (m-80) cc_final: 0.7425 (m-80) REVERT: B 548 MET cc_start: 0.8659 (mtt) cc_final: 0.8455 (mtp) REVERT: B 617 LEU cc_start: 0.7713 (mt) cc_final: 0.7421 (mm) REVERT: B 621 PHE cc_start: 0.8295 (m-80) cc_final: 0.7958 (m-80) REVERT: B 623 LYS cc_start: 0.7016 (mptt) cc_final: 0.6771 (mmtm) REVERT: B 652 ARG cc_start: 0.5975 (mmt180) cc_final: 0.4767 (mtm180) REVERT: B 738 LYS cc_start: 0.8221 (ptpp) cc_final: 0.7853 (mtpp) REVERT: B 783 ILE cc_start: 0.8541 (tt) cc_final: 0.8327 (pt) REVERT: B 814 ASP cc_start: 0.7689 (m-30) cc_final: 0.7393 (m-30) outliers start: 18 outliers final: 5 residues processed: 162 average time/residue: 1.0350 time to fit residues: 183.9116 Evaluate side-chains 143 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 635 ILE Chi-restraints excluded: chain A residue 650 MET Chi-restraints excluded: chain A residue 821 ARG Chi-restraints excluded: chain B residue 124 GLU 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 81 optimal weight: 1.9990 chunk 51 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 113 GLN B 497 ASN B 541 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.100225 restraints weight = 12386.452| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.19 r_work: 0.3115 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 11408 Z= 0.314 Angle : 0.674 6.863 15488 Z= 0.357 Chirality : 0.049 0.223 1732 Planarity : 0.004 0.054 1920 Dihedral : 9.481 91.275 1570 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.07 % Allowed : 10.84 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1348 helix: 0.83 (0.21), residues: 604 sheet: 1.27 (0.28), residues: 278 loop : -1.93 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 629 HIS 0.004 0.001 HIS B 795 PHE 0.020 0.002 PHE B 632 TYR 0.021 0.002 TYR A 724 ARG 0.004 0.001 ARG B 821 Details of bonding type rmsd hydrogen bonds : bond 0.05913 ( 614) hydrogen bonds : angle 4.72079 ( 1746) metal coordination : bond 0.01364 ( 6) SS BOND : bond 0.00314 ( 8) SS BOND : angle 2.05869 ( 16) covalent geometry : bond 0.00747 (11394) covalent geometry : angle 0.67068 (15472) *********************** 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 178 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6501 (mmm-85) cc_final: 0.5856 (ttp-170) REVERT: A 63 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.7943 (tp) REVERT: A 90 ASN cc_start: 0.8149 (m-40) cc_final: 0.7792 (m-40) REVERT: A 118 ARG cc_start: 0.7888 (ttm110) cc_final: 0.7156 (ttt90) REVERT: A 143 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8208 (mt0) REVERT: A 145 ILE cc_start: 0.9070 (mt) cc_final: 0.8790 (mp) REVERT: A 540 LYS cc_start: 0.8340 (mttm) cc_final: 0.7915 (mmtt) REVERT: A 650 MET cc_start: 0.7174 (mtt) cc_final: 0.6578 (mtp) REVERT: B 44 ARG cc_start: 0.7117 (mmm-85) cc_final: 0.6802 (ttt-90) REVERT: B 195 LYS cc_start: 0.8561 (mppt) cc_final: 0.8345 (tppt) REVERT: B 207 GLU cc_start: 0.7540 (mp0) cc_final: 0.7133 (mp0) REVERT: B 221 MET cc_start: 0.8159 (mtp) cc_final: 0.7344 (mpt) REVERT: B 446 TRP cc_start: 0.6370 (OUTLIER) cc_final: 0.5485 (m100) REVERT: B 536 TYR cc_start: 0.7625 (m-80) cc_final: 0.7339 (m-80) REVERT: B 617 LEU cc_start: 0.7743 (mt) cc_final: 0.7453 (mm) REVERT: B 621 PHE cc_start: 0.8495 (m-80) cc_final: 0.8085 (m-80) REVERT: B 623 LYS cc_start: 0.7699 (mptt) cc_final: 0.7345 (mmtm) REVERT: B 650 MET cc_start: 0.7015 (OUTLIER) cc_final: 0.6305 (mtt) REVERT: B 652 ARG cc_start: 0.6690 (mmt180) cc_final: 0.5334 (mtt180) REVERT: B 700 PHE cc_start: 0.6672 (t80) cc_final: 0.6370 (t80) REVERT: B 783 ILE cc_start: 0.8543 (tt) cc_final: 0.8337 (pt) outliers start: 25 outliers final: 9 residues processed: 164 average time/residue: 1.2725 time to fit residues: 228.1601 Evaluate side-chains 151 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 1.224 ------------------------------------------------------------------------------- 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 221 MET Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 607 SER 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 650 MET Chi-restraints excluded: chain B residue 818 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 81 optimal weight: 2.9990 chunk 84 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 132 optimal weight: 0.8980 chunk 29 optimal weight: 9.9990 chunk 74 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 447 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 447 ASN B 779 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.155986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104111 restraints weight = 12189.172| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.30 r_work: 0.3180 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11408 Z= 0.127 Angle : 0.505 6.134 15488 Z= 0.271 Chirality : 0.043 0.141 1732 Planarity : 0.003 0.031 1920 Dihedral : 8.658 84.259 1570 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.82 % Allowed : 12.50 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1348 helix: 1.30 (0.21), residues: 606 sheet: 1.32 (0.29), residues: 282 loop : -1.92 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.012 0.001 PHE B 632 TYR 0.014 0.001 TYR A 210 ARG 0.003 0.000 ARG A 593 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 614) hydrogen bonds : angle 4.24341 ( 1746) metal coordination : bond 0.00696 ( 6) SS BOND : bond 0.00276 ( 8) SS BOND : angle 1.69982 ( 16) covalent geometry : bond 0.00283 (11394) covalent geometry : angle 0.50272 (15472) *********************** 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 174 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 152 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6725 (mmm-85) cc_final: 0.6290 (ttp-170) REVERT: A 63 ILE cc_start: 0.8426 (mm) cc_final: 0.7845 (tp) REVERT: A 90 ASN cc_start: 0.7999 (m-40) cc_final: 0.7652 (m-40) REVERT: A 118 ARG cc_start: 0.7822 (ttm110) cc_final: 0.7113 (ttt90) REVERT: A 143 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: A 145 ILE cc_start: 0.9045 (mt) cc_final: 0.8762 (mp) REVERT: A 536 TYR cc_start: 0.7220 (m-80) cc_final: 0.6677 (m-80) REVERT: A 540 LYS cc_start: 0.8187 (mttm) cc_final: 0.7834 (mmtt) REVERT: A 554 MET cc_start: 0.8271 (tpp) cc_final: 0.7923 (mmt) REVERT: A 707 ARG cc_start: 0.7874 (tpt-90) cc_final: 0.7263 (mtp180) REVERT: B 44 ARG cc_start: 0.7010 (mmm-85) cc_final: 0.6515 (tmt90) REVERT: B 71 GLN cc_start: 0.7826 (mm-40) cc_final: 0.7381 (mp-120) REVERT: B 83 ASN cc_start: 0.7934 (p0) cc_final: 0.7669 (p0) REVERT: B 118 ARG cc_start: 0.7655 (ttm-80) cc_final: 0.7257 (mtp180) REVERT: B 221 MET cc_start: 0.7869 (mtp) cc_final: 0.7305 (mpm) REVERT: B 446 TRP cc_start: 0.6444 (OUTLIER) cc_final: 0.5465 (m100) REVERT: B 519 ASP cc_start: 0.8660 (t0) cc_final: 0.8416 (t0) REVERT: B 523 ARG cc_start: 0.6260 (mtp180) cc_final: 0.4943 (mtt90) REVERT: B 536 TYR cc_start: 0.7499 (m-80) cc_final: 0.7220 (m-80) REVERT: B 621 PHE cc_start: 0.8516 (m-80) cc_final: 0.8182 (m-80) REVERT: B 623 LYS cc_start: 0.7219 (mptt) cc_final: 0.6933 (mmtm) REVERT: B 650 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6500 (mtt) REVERT: B 652 ARG cc_start: 0.6552 (mmt180) cc_final: 0.5254 (mtm110) REVERT: B 700 PHE cc_start: 0.6556 (t80) cc_final: 0.6262 (t80) outliers start: 22 outliers final: 8 residues processed: 166 average time/residue: 1.4178 time to fit residues: 261.6912 Evaluate side-chains 150 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 1.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL 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 449 ILE Chi-restraints excluded: chain B residue 613 MET 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 44 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 447 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.153489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.104080 restraints weight = 12246.630| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.19 r_work: 0.3168 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11408 Z= 0.147 Angle : 0.516 7.153 15488 Z= 0.275 Chirality : 0.043 0.150 1732 Planarity : 0.003 0.032 1920 Dihedral : 8.428 83.663 1570 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.24 % Allowed : 12.75 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1348 helix: 1.37 (0.21), residues: 612 sheet: 1.38 (0.29), residues: 282 loop : -1.85 (0.27), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.003 0.001 HIS B 594 PHE 0.013 0.001 PHE B 632 TYR 0.014 0.001 TYR A 188 ARG 0.003 0.000 ARG A 821 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 614) hydrogen bonds : angle 4.19737 ( 1746) metal coordination : bond 0.00754 ( 6) SS BOND : bond 0.00200 ( 8) SS BOND : angle 1.10536 ( 16) covalent geometry : bond 0.00337 (11394) covalent geometry : angle 0.51488 (15472) *********************** 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 176 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6520 (mmm-85) cc_final: 0.6215 (ttp-170) REVERT: A 63 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.7810 (tp) REVERT: A 90 ASN cc_start: 0.8060 (m-40) cc_final: 0.7719 (m-40) REVERT: A 118 ARG cc_start: 0.7805 (ttm110) cc_final: 0.7126 (ttt90) REVERT: A 143 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8131 (mt0) REVERT: A 145 ILE cc_start: 0.9045 (mt) cc_final: 0.8778 (mp) REVERT: A 536 TYR cc_start: 0.7223 (m-80) cc_final: 0.6625 (m-80) REVERT: A 540 LYS cc_start: 0.8276 (mttm) cc_final: 0.7930 (mmtt) REVERT: A 554 MET cc_start: 0.8287 (tpp) cc_final: 0.7964 (mmt) REVERT: A 602 TYR cc_start: 0.4523 (OUTLIER) cc_final: 0.3083 (m-80) REVERT: A 613 MET cc_start: 0.8016 (tpt) cc_final: 0.7615 (mmm) REVERT: A 681 MET cc_start: 0.4912 (OUTLIER) cc_final: 0.4478 (tpt) REVERT: A 707 ARG cc_start: 0.7930 (tpt-90) cc_final: 0.7347 (mtp180) REVERT: B 44 ARG cc_start: 0.7012 (mmm-85) cc_final: 0.6586 (tmt90) REVERT: B 83 ASN cc_start: 0.8148 (p0) cc_final: 0.7804 (p0) REVERT: B 118 ARG cc_start: 0.7664 (ttm-80) cc_final: 0.7298 (mtp180) REVERT: B 143 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7726 (mm110) REVERT: B 446 TRP cc_start: 0.6510 (OUTLIER) cc_final: 0.5551 (m100) REVERT: B 536 TYR cc_start: 0.7474 (m-80) cc_final: 0.7212 (m-80) REVERT: B 621 PHE cc_start: 0.8509 (m-80) cc_final: 0.8243 (m-80) REVERT: B 623 LYS cc_start: 0.7315 (mptt) cc_final: 0.7017 (mmtm) REVERT: B 650 MET cc_start: 0.6703 (OUTLIER) cc_final: 0.6435 (mtt) REVERT: B 652 ARG cc_start: 0.6617 (mmt180) cc_final: 0.5302 (mtm110) REVERT: B 700 PHE cc_start: 0.6560 (t80) cc_final: 0.6227 (t80) outliers start: 27 outliers final: 12 residues processed: 164 average time/residue: 1.1311 time to fit residues: 204.7746 Evaluate side-chains 158 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.124 ------------------------------------------------------------------------------- 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 681 MET 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 143 GLN 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 650 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 GLN A 691 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.151150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101508 restraints weight = 12363.923| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.20 r_work: 0.3131 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 11408 Z= 0.239 Angle : 0.602 8.338 15488 Z= 0.319 Chirality : 0.046 0.201 1732 Planarity : 0.004 0.045 1920 Dihedral : 8.636 87.811 1570 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.48 % Allowed : 12.50 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1348 helix: 1.13 (0.21), residues: 618 sheet: 1.46 (0.28), residues: 282 loop : -1.68 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 629 HIS 0.003 0.001 HIS B 795 PHE 0.018 0.002 PHE B 632 TYR 0.017 0.002 TYR B 759 ARG 0.004 0.000 ARG A 821 Details of bonding type rmsd hydrogen bonds : bond 0.05281 ( 614) hydrogen bonds : angle 4.41502 ( 1746) metal coordination : bond 0.00975 ( 6) SS BOND : bond 0.00245 ( 8) SS BOND : angle 2.14858 ( 16) covalent geometry : bond 0.00564 (11394) covalent geometry : angle 0.59787 (15472) *********************** 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 176 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6534 (mmm-85) cc_final: 0.6211 (ttp-170) REVERT: A 63 ILE cc_start: 0.8556 (OUTLIER) cc_final: 0.7906 (tp) REVERT: A 90 ASN cc_start: 0.8188 (m-40) cc_final: 0.7847 (m-40) REVERT: A 118 ARG cc_start: 0.7834 (ttm110) cc_final: 0.7156 (ttt90) REVERT: A 143 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: A 145 ILE cc_start: 0.9050 (mt) cc_final: 0.8770 (mp) REVERT: A 536 TYR cc_start: 0.7321 (m-80) cc_final: 0.6696 (m-80) REVERT: A 540 LYS cc_start: 0.8340 (mttm) cc_final: 0.7958 (mmmt) REVERT: A 554 MET cc_start: 0.8294 (tpp) cc_final: 0.7997 (mmt) REVERT: A 602 TYR cc_start: 0.4407 (OUTLIER) cc_final: 0.3122 (m-80) REVERT: A 613 MET cc_start: 0.8013 (tpt) cc_final: 0.7565 (mmm) REVERT: A 707 ARG cc_start: 0.7986 (tpt-90) cc_final: 0.7421 (mtp180) REVERT: B 44 ARG cc_start: 0.7089 (mmm-85) cc_final: 0.6741 (ttt-90) REVERT: B 118 ARG cc_start: 0.7656 (ttm-80) cc_final: 0.7229 (mtp180) REVERT: B 221 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7174 (mpm) REVERT: B 276 PHE cc_start: 0.6491 (OUTLIER) cc_final: 0.5270 (t80) REVERT: B 536 TYR cc_start: 0.7537 (m-80) cc_final: 0.7240 (m-80) REVERT: B 621 PHE cc_start: 0.8472 (m-80) cc_final: 0.8125 (m-80) REVERT: B 623 LYS cc_start: 0.7577 (mptt) cc_final: 0.7258 (mmtm) REVERT: B 650 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6474 (mtt) REVERT: B 652 ARG cc_start: 0.6838 (mmt180) cc_final: 0.5429 (mtm110) REVERT: B 700 PHE cc_start: 0.6666 (t80) cc_final: 0.6252 (t80) REVERT: B 704 TYR cc_start: 0.7869 (m-80) cc_final: 0.7531 (m-80) outliers start: 30 outliers final: 13 residues processed: 162 average time/residue: 1.0463 time to fit residues: 185.8290 Evaluate side-chains 159 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 140 time to evaluate : 1.110 ------------------------------------------------------------------------------- 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 610 VAL 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 221 MET Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 613 MET 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 126 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN A 278 GLN A 691 ASN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.151286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.101703 restraints weight = 12435.246| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.20 r_work: 0.3134 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11408 Z= 0.224 Angle : 0.581 7.632 15488 Z= 0.309 Chirality : 0.046 0.196 1732 Planarity : 0.004 0.041 1920 Dihedral : 8.487 86.896 1570 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.48 % Allowed : 13.16 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1348 helix: 1.16 (0.21), residues: 618 sheet: 1.49 (0.28), residues: 282 loop : -1.64 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 629 HIS 0.003 0.001 HIS B 229 PHE 0.017 0.002 PHE B 632 TYR 0.017 0.002 TYR A 724 ARG 0.005 0.000 ARG A 821 Details of bonding type rmsd hydrogen bonds : bond 0.05126 ( 614) hydrogen bonds : angle 4.39870 ( 1746) metal coordination : bond 0.00991 ( 6) SS BOND : bond 0.00268 ( 8) SS BOND : angle 1.69831 ( 16) covalent geometry : bond 0.00528 (11394) covalent geometry : angle 0.57836 (15472) *********************** 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 171 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6528 (mmm-85) cc_final: 0.6242 (ttp-170) REVERT: A 63 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.7893 (tp) REVERT: A 90 ASN cc_start: 0.8089 (m-40) cc_final: 0.7769 (m-40) REVERT: A 118 ARG cc_start: 0.7830 (ttm110) cc_final: 0.7150 (ttt90) REVERT: A 143 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: A 145 ILE cc_start: 0.9054 (mt) cc_final: 0.8776 (mp) REVERT: A 278 GLN cc_start: 0.4217 (OUTLIER) cc_final: 0.3803 (tm-30) REVERT: A 536 TYR cc_start: 0.7198 (m-80) cc_final: 0.6654 (m-80) REVERT: A 540 LYS cc_start: 0.8363 (mttm) cc_final: 0.7981 (mmmt) REVERT: A 554 MET cc_start: 0.8335 (tpp) cc_final: 0.8016 (mmt) REVERT: A 602 TYR cc_start: 0.4657 (OUTLIER) cc_final: 0.4046 (t80) REVERT: A 707 ARG cc_start: 0.7996 (tpt-90) cc_final: 0.7437 (mtp180) REVERT: B 44 ARG cc_start: 0.7140 (mmm-85) cc_final: 0.6749 (ttt-90) REVERT: B 71 GLN cc_start: 0.7887 (mm-40) cc_final: 0.7409 (mp-120) REVERT: B 118 ARG cc_start: 0.7697 (ttm-80) cc_final: 0.7267 (mtp180) REVERT: B 133 GLU cc_start: 0.7057 (tt0) cc_final: 0.6637 (tt0) REVERT: B 276 PHE cc_start: 0.6597 (OUTLIER) cc_final: 0.5572 (t80) REVERT: B 446 TRP cc_start: 0.6478 (OUTLIER) cc_final: 0.5470 (m100) REVERT: B 536 TYR cc_start: 0.7499 (m-80) cc_final: 0.7210 (m-80) REVERT: B 621 PHE cc_start: 0.8455 (m-80) cc_final: 0.8110 (m-80) REVERT: B 623 LYS cc_start: 0.7547 (mptt) cc_final: 0.7200 (mmtm) REVERT: B 650 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6055 (mtp) REVERT: B 652 ARG cc_start: 0.6705 (mmt180) cc_final: 0.5220 (mtm110) REVERT: B 700 PHE cc_start: 0.6696 (t80) cc_final: 0.6242 (t80) REVERT: B 704 TYR cc_start: 0.7910 (m-80) cc_final: 0.7560 (m-80) outliers start: 30 outliers final: 14 residues processed: 160 average time/residue: 1.0299 time to fit residues: 180.4453 Evaluate side-chains 155 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 1.118 ------------------------------------------------------------------------------- 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 278 GLN Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 607 SER Chi-restraints excluded: chain A residue 610 VAL 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 276 PHE Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 449 ILE Chi-restraints excluded: chain B residue 469 VAL 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 113 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 28 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** 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 = 0.3920 r_free = 0.3920 target = 0.152780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.103376 restraints weight = 12327.353| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.21 r_work: 0.3157 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3206 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= 0.160 Angle : 0.548 8.832 15488 Z= 0.290 Chirality : 0.044 0.163 1732 Planarity : 0.003 0.035 1920 Dihedral : 8.242 84.950 1570 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.24 % Allowed : 13.58 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1348 helix: 1.30 (0.21), residues: 618 sheet: 1.42 (0.28), residues: 282 loop : -1.67 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.003 0.001 HIS A 636 PHE 0.014 0.001 PHE B 632 TYR 0.014 0.002 TYR A 188 ARG 0.005 0.000 ARG A 821 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 614) hydrogen bonds : angle 4.29383 ( 1746) metal coordination : bond 0.00806 ( 6) SS BOND : bond 0.00165 ( 8) SS BOND : angle 2.38868 ( 16) covalent geometry : bond 0.00370 (11394) covalent geometry : angle 0.54249 (15472) *********************** 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 167 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6529 (mmm-85) cc_final: 0.6243 (ttp-170) REVERT: A 63 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.7837 (tp) REVERT: A 90 ASN cc_start: 0.8085 (m-40) cc_final: 0.7768 (m-40) REVERT: A 118 ARG cc_start: 0.7831 (ttm110) cc_final: 0.7152 (ttt90) REVERT: A 143 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: A 145 ILE cc_start: 0.9039 (mt) cc_final: 0.8762 (mp) REVERT: A 536 TYR cc_start: 0.7195 (m-80) cc_final: 0.6659 (m-80) REVERT: A 540 LYS cc_start: 0.8334 (mttm) cc_final: 0.7953 (mmtt) REVERT: A 554 MET cc_start: 0.8225 (tpp) cc_final: 0.7921 (mmt) REVERT: A 602 TYR cc_start: 0.4641 (OUTLIER) cc_final: 0.4101 (t80) REVERT: A 613 MET cc_start: 0.8018 (tpt) cc_final: 0.7593 (mmm) REVERT: A 650 MET cc_start: 0.7507 (mtp) cc_final: 0.7256 (mtt) REVERT: A 707 ARG cc_start: 0.7960 (tpt-90) cc_final: 0.7469 (mtp180) REVERT: B 44 ARG cc_start: 0.7150 (mmm-85) cc_final: 0.6758 (ttt-90) REVERT: B 83 ASN cc_start: 0.8174 (p0) cc_final: 0.7845 (p0) REVERT: B 118 ARG cc_start: 0.7669 (ttm-80) cc_final: 0.7251 (mtp180) REVERT: B 133 GLU cc_start: 0.7047 (tt0) cc_final: 0.6557 (tt0) REVERT: B 207 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7979 (mp0) REVERT: B 276 PHE cc_start: 0.6478 (OUTLIER) cc_final: 0.5416 (t80) REVERT: B 446 TRP cc_start: 0.6541 (OUTLIER) cc_final: 0.5564 (m100) REVERT: B 536 TYR cc_start: 0.7463 (m-80) cc_final: 0.7192 (m-80) REVERT: B 621 PHE cc_start: 0.8442 (m-80) cc_final: 0.8128 (m-80) REVERT: B 623 LYS cc_start: 0.7304 (mptt) cc_final: 0.6953 (mmtm) REVERT: B 650 MET cc_start: 0.6783 (OUTLIER) cc_final: 0.6416 (mtp) REVERT: B 652 ARG cc_start: 0.6653 (mmt180) cc_final: 0.6171 (mpt180) REVERT: B 700 PHE cc_start: 0.6738 (t80) cc_final: 0.6240 (t80) REVERT: B 704 TYR cc_start: 0.7888 (m-80) cc_final: 0.7534 (m-80) outliers start: 27 outliers final: 13 residues processed: 158 average time/residue: 1.1453 time to fit residues: 199.0797 Evaluate side-chains 155 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 135 time to evaluate : 2.028 ------------------------------------------------------------------------------- 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 221 MET 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 617 LEU 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 207 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 650 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 35 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 94 optimal weight: 0.7980 chunk 128 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 115 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 158 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.157803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.108892 restraints weight = 13048.958| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.22 r_work: 0.3377 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11408 Z= 0.157 Angle : 0.534 6.528 15488 Z= 0.284 Chirality : 0.043 0.163 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.036 83.422 1570 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.82 % Allowed : 14.32 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.23), residues: 1348 helix: 1.35 (0.21), residues: 618 sheet: 1.47 (0.28), residues: 286 loop : -1.66 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.003 0.001 HIS A 636 PHE 0.014 0.001 PHE B 632 TYR 0.014 0.002 TYR A 188 ARG 0.003 0.000 ARG B 821 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 614) hydrogen bonds : angle 4.26477 ( 1746) metal coordination : bond 0.00776 ( 6) SS BOND : bond 0.00170 ( 8) SS BOND : angle 1.46653 ( 16) covalent geometry : bond 0.00361 (11394) covalent geometry : angle 0.53266 (15472) *********************** 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 160 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 1.166 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6716 (mmm-85) cc_final: 0.6428 (ttp-170) REVERT: A 63 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.7953 (tp) REVERT: A 90 ASN cc_start: 0.8096 (m-40) cc_final: 0.7806 (m-40) REVERT: A 118 ARG cc_start: 0.7884 (ttm110) cc_final: 0.7318 (ttt90) REVERT: A 143 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8198 (mt0) REVERT: A 145 ILE cc_start: 0.9127 (mt) cc_final: 0.8879 (mp) REVERT: A 536 TYR cc_start: 0.7356 (m-80) cc_final: 0.6777 (m-80) REVERT: A 540 LYS cc_start: 0.8352 (mttm) cc_final: 0.7983 (mmtt) REVERT: A 554 MET cc_start: 0.8260 (tpp) cc_final: 0.8001 (mmt) REVERT: A 602 TYR cc_start: 0.4655 (OUTLIER) cc_final: 0.4100 (t80) REVERT: A 613 MET cc_start: 0.8165 (tpt) cc_final: 0.7752 (mmm) REVERT: A 650 MET cc_start: 0.7514 (mtp) cc_final: 0.7274 (mtt) REVERT: B 44 ARG cc_start: 0.7234 (mmm-85) cc_final: 0.6840 (ttt-90) REVERT: B 71 GLN cc_start: 0.8047 (mm-40) cc_final: 0.7615 (mp-120) REVERT: B 83 ASN cc_start: 0.8231 (p0) cc_final: 0.7949 (p0) REVERT: B 118 ARG cc_start: 0.7761 (ttm-80) cc_final: 0.7392 (mtp180) REVERT: B 133 GLU cc_start: 0.7033 (tt0) cc_final: 0.6569 (tt0) REVERT: B 207 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: B 276 PHE cc_start: 0.6462 (OUTLIER) cc_final: 0.5288 (t80) REVERT: B 446 TRP cc_start: 0.6627 (OUTLIER) cc_final: 0.5613 (m100) REVERT: B 447 ASN cc_start: 0.7109 (m-40) cc_final: 0.6845 (t0) REVERT: B 536 TYR cc_start: 0.7547 (m-80) cc_final: 0.7267 (m-80) REVERT: B 621 PHE cc_start: 0.8492 (m-80) cc_final: 0.8220 (m-80) REVERT: B 623 LYS cc_start: 0.7312 (mptt) cc_final: 0.6999 (mmtm) REVERT: B 652 ARG cc_start: 0.6822 (mmt180) cc_final: 0.6334 (mpt180) REVERT: B 700 PHE cc_start: 0.6822 (t80) cc_final: 0.6339 (t80) REVERT: B 704 TYR cc_start: 0.7978 (m-80) cc_final: 0.7640 (m-80) outliers start: 22 outliers final: 14 residues processed: 152 average time/residue: 1.1219 time to fit residues: 188.0696 Evaluate side-chains 157 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.192 ------------------------------------------------------------------------------- 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 221 MET 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 617 LEU 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 207 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 613 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 131 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 51 optimal weight: 9.9990 chunk 107 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 112 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.158641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.109610 restraints weight = 13110.014| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.23 r_work: 0.3372 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11408 Z= 0.139 Angle : 0.529 8.245 15488 Z= 0.278 Chirality : 0.043 0.154 1732 Planarity : 0.003 0.034 1920 Dihedral : 7.867 81.974 1570 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.74 % Allowed : 14.16 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1348 helix: 1.53 (0.21), residues: 610 sheet: 1.48 (0.28), residues: 286 loop : -1.52 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 629 HIS 0.003 0.001 HIS A 636 PHE 0.013 0.001 PHE B 632 TYR 0.013 0.001 TYR A 188 ARG 0.005 0.000 ARG A 705 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 614) hydrogen bonds : angle 4.17381 ( 1746) metal coordination : bond 0.00718 ( 6) SS BOND : bond 0.00152 ( 8) SS BOND : angle 2.22391 ( 16) covalent geometry : bond 0.00315 (11394) covalent geometry : angle 0.52412 (15472) ********************** 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 163 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.520 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6787 (mmm-85) cc_final: 0.6557 (ttp-170) REVERT: A 63 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.7895 (tp) REVERT: A 90 ASN cc_start: 0.8105 (m-40) cc_final: 0.7804 (m-40) REVERT: A 118 ARG cc_start: 0.7864 (ttm110) cc_final: 0.7251 (ttt90) REVERT: A 143 GLN cc_start: 0.8865 (OUTLIER) cc_final: 0.8165 (mt0) REVERT: A 145 ILE cc_start: 0.9107 (mt) cc_final: 0.8854 (mp) REVERT: A 536 TYR cc_start: 0.7344 (m-80) cc_final: 0.6755 (m-80) REVERT: A 540 LYS cc_start: 0.8339 (mttm) cc_final: 0.7965 (mmtt) REVERT: A 554 MET cc_start: 0.8189 (tpp) cc_final: 0.7961 (mmt) REVERT: A 602 TYR cc_start: 0.4690 (OUTLIER) cc_final: 0.4146 (t80) REVERT: A 613 MET cc_start: 0.8154 (tpt) cc_final: 0.7731 (mmm) REVERT: A 625 ASP cc_start: 0.6740 (t0) cc_final: 0.6432 (t0) REVERT: A 650 MET cc_start: 0.7490 (mtp) cc_final: 0.7255 (mtt) REVERT: A 707 ARG cc_start: 0.8027 (tpt-90) cc_final: 0.7548 (mtp180) REVERT: B 44 ARG cc_start: 0.7218 (mmm-85) cc_final: 0.6805 (ttt-90) REVERT: B 71 GLN cc_start: 0.8015 (mm-40) cc_final: 0.7553 (mp-120) REVERT: B 83 ASN cc_start: 0.8160 (p0) cc_final: 0.7897 (p0) REVERT: B 118 ARG cc_start: 0.7744 (ttm-80) cc_final: 0.7369 (mtp180) REVERT: B 133 GLU cc_start: 0.6963 (tt0) cc_final: 0.6471 (tt0) REVERT: B 221 MET cc_start: 0.8124 (mmm) cc_final: 0.6859 (mpm) REVERT: B 276 PHE cc_start: 0.6365 (OUTLIER) cc_final: 0.5159 (t80) REVERT: B 446 TRP cc_start: 0.6603 (OUTLIER) cc_final: 0.5623 (m100) REVERT: B 536 TYR cc_start: 0.7439 (m-80) cc_final: 0.7196 (m-80) REVERT: B 621 PHE cc_start: 0.8476 (m-80) cc_final: 0.8218 (m-80) REVERT: B 623 LYS cc_start: 0.7209 (mptt) cc_final: 0.6926 (mmtm) REVERT: B 652 ARG cc_start: 0.6918 (mmt180) cc_final: 0.5491 (mtm110) REVERT: B 700 PHE cc_start: 0.6807 (t80) cc_final: 0.6301 (t80) REVERT: B 704 TYR cc_start: 0.7987 (m-80) cc_final: 0.7568 (m-10) outliers start: 21 outliers final: 11 residues processed: 155 average time/residue: 1.4891 time to fit residues: 252.5989 Evaluate side-chains 154 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 138 time to evaluate : 1.256 ------------------------------------------------------------------------------- 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 B residue 76 THR Chi-restraints excluded: chain B residue 124 GLU Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 276 PHE Chi-restraints excluded: chain B residue 446 TRP Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 613 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 90 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.160126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111129 restraints weight = 12911.117| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.23 r_work: 0.3405 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3296 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.3410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11408 Z= 0.112 Angle : 0.496 6.337 15488 Z= 0.263 Chirality : 0.042 0.147 1732 Planarity : 0.003 0.033 1920 Dihedral : 7.558 78.812 1570 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.49 % Allowed : 14.40 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1348 helix: 1.64 (0.21), residues: 610 sheet: 1.52 (0.29), residues: 282 loop : -1.50 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 629 HIS 0.004 0.001 HIS A 636 PHE 0.013 0.001 PHE B 632 TYR 0.013 0.001 TYR A 210 ARG 0.008 0.000 ARG A 821 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 614) hydrogen bonds : angle 4.07620 ( 1746) metal coordination : bond 0.00579 ( 6) SS BOND : bond 0.00150 ( 8) SS BOND : angle 1.10451 ( 16) covalent geometry : bond 0.00245 (11394) covalent geometry : angle 0.49457 (15472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11951.84 seconds wall clock time: 218 minutes 54.43 seconds (13134.43 seconds total)