Starting phenix.real_space_refine on Sun Dec 29 20:35:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jun_36662/12_2024/8jun_36662.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jun_36662/12_2024/8jun_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_36662/12_2024/8jun_36662.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jun_36662/12_2024/8jun_36662.map" model { file = "/net/cci-nas-00/data/ceres_data/8jun_36662/12_2024/8jun_36662.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jun_36662/12_2024/8jun_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-5532/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: 6.22, per 1000 atoms: 0.56 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: 2.96 Conformation dependent library (CDL) restraints added in 1.5 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: 1.06 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: 3.44 Time building geometry restraints manager: 3.39 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.960 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.100 ------------------------------------------------------------------------------- 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 : 0.007 0.137 11394 Z= 0.443 Angle : 1.000 29.441 15472 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 *********************** 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 : 1.226 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: 1.1734 time to fit residues: 247.8545 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 : 1.272 ------------------------------------------------------------------------------- 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: 4.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 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 11394 Z= 0.239 Angle : 0.558 7.444 15472 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 *********************** 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 : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6473 (mmm-85) cc_final: 0.6000 (ttp-170) REVERT: A 145 ILE cc_start: 0.9057 (mt) cc_final: 0.8814 (mp) REVERT: A 536 TYR cc_start: 0.7335 (m-80) cc_final: 0.6853 (m-80) REVERT: A 650 MET cc_start: 0.6893 (OUTLIER) cc_final: 0.6601 (mtt) REVERT: B 44 ARG cc_start: 0.6880 (mmm-85) cc_final: 0.6410 (tmt170) REVERT: B 83 ASN cc_start: 0.7561 (p0) cc_final: 0.7285 (p0) REVERT: B 115 LEU cc_start: 0.8516 (mt) cc_final: 0.8248 (mt) REVERT: B 207 GLU cc_start: 0.7034 (mp0) cc_final: 0.6815 (mp0) REVERT: B 536 TYR cc_start: 0.7950 (m-80) cc_final: 0.7660 (m-80) REVERT: B 548 MET cc_start: 0.8470 (mtt) cc_final: 0.8242 (mtp) REVERT: B 617 LEU cc_start: 0.7782 (mt) cc_final: 0.7520 (mm) REVERT: B 621 PHE cc_start: 0.8408 (m-80) cc_final: 0.8115 (m-80) REVERT: B 652 ARG cc_start: 0.6382 (mmt180) cc_final: 0.5282 (mtm180) REVERT: B 738 LYS cc_start: 0.8216 (ptpp) cc_final: 0.7895 (mtpp) REVERT: B 814 ASP cc_start: 0.7719 (m-30) cc_final: 0.7429 (m-30) outliers start: 18 outliers final: 5 residues processed: 162 average time/residue: 1.0718 time to fit residues: 190.6538 Evaluate side-chains 144 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 1.236 ------------------------------------------------------------------------------- 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 67 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 108 optimal weight: 5.9990 chunk 120 optimal weight: 9.9990 chunk 41 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 11394 Z= 0.484 Angle : 0.669 6.578 15472 Z= 0.355 Chirality : 0.049 0.226 1732 Planarity : 0.004 0.054 1920 Dihedral : 9.481 91.148 1570 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.15 % Allowed : 11.09 % Favored : 86.75 % 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: 0.02 (0.22), residues: 1348 helix: 0.84 (0.21), residues: 604 sheet: 1.28 (0.28), residues: 278 loop : -1.93 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 629 HIS 0.004 0.001 HIS B 795 PHE 0.020 0.002 PHE B 632 TYR 0.021 0.003 TYR A 724 ARG 0.005 0.001 ARG B 821 *********************** 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 176 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6440 (mmm-85) cc_final: 0.6195 (ttp-170) REVERT: A 63 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8009 (tp) REVERT: A 90 ASN cc_start: 0.8076 (m-40) cc_final: 0.7763 (m-40) REVERT: A 143 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8017 (mt0) REVERT: A 145 ILE cc_start: 0.9054 (mt) cc_final: 0.8798 (mp) REVERT: A 540 LYS cc_start: 0.8229 (mttm) cc_final: 0.7897 (mmtt) REVERT: A 650 MET cc_start: 0.7043 (mtt) cc_final: 0.6516 (mtp) REVERT: B 115 LEU cc_start: 0.8516 (mt) cc_final: 0.8315 (mt) REVERT: B 207 GLU cc_start: 0.6994 (mp0) cc_final: 0.6717 (mp0) REVERT: B 221 MET cc_start: 0.7089 (mtp) cc_final: 0.6698 (mpt) REVERT: B 446 TRP cc_start: 0.5966 (OUTLIER) cc_final: 0.5419 (m100) REVERT: B 536 TYR cc_start: 0.7791 (m-80) cc_final: 0.7504 (m-80) REVERT: B 617 LEU cc_start: 0.7773 (mt) cc_final: 0.7518 (mm) REVERT: B 621 PHE cc_start: 0.8613 (m-80) cc_final: 0.8258 (m-80) REVERT: B 650 MET cc_start: 0.6939 (OUTLIER) cc_final: 0.6254 (mtt) REVERT: B 652 ARG cc_start: 0.7009 (mmt180) cc_final: 0.5815 (mtt180) outliers start: 26 outliers final: 9 residues processed: 162 average time/residue: 1.1681 time to fit residues: 206.1735 Evaluate side-chains 148 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 120 optimal weight: 20.0000 chunk 91 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11394 Z= 0.267 Angle : 0.543 5.762 15472 Z= 0.291 Chirality : 0.044 0.168 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.993 87.242 1570 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.07 % Allowed : 12.33 % Favored : 85.60 % 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: 0.29 (0.23), residues: 1348 helix: 1.18 (0.21), residues: 606 sheet: 1.31 (0.29), residues: 282 loop : -1.94 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.013 0.002 PHE B 632 TYR 0.014 0.002 TYR A 188 ARG 0.005 0.000 ARG B 44 *********************** 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 173 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8479 (OUTLIER) cc_final: 0.7950 (tp) REVERT: A 90 ASN cc_start: 0.8004 (m-40) cc_final: 0.7704 (m-40) REVERT: A 143 GLN cc_start: 0.8693 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: A 145 ILE cc_start: 0.9033 (mt) cc_final: 0.8780 (mp) REVERT: A 536 TYR cc_start: 0.7471 (m-80) cc_final: 0.7017 (m-80) REVERT: A 540 LYS cc_start: 0.8126 (mttm) cc_final: 0.7866 (mmtt) REVERT: A 554 MET cc_start: 0.7387 (tpp) cc_final: 0.7093 (mmt) REVERT: B 83 ASN cc_start: 0.7748 (p0) cc_final: 0.7420 (p0) REVERT: B 207 GLU cc_start: 0.6960 (mp0) cc_final: 0.6672 (mp0) REVERT: B 536 TYR cc_start: 0.7769 (m-80) cc_final: 0.7442 (m-80) REVERT: B 548 MET cc_start: 0.8447 (mtm) cc_final: 0.8231 (mtp) REVERT: B 621 PHE cc_start: 0.8557 (m-80) cc_final: 0.8229 (m-80) REVERT: B 650 MET cc_start: 0.6881 (OUTLIER) cc_final: 0.6456 (mtt) REVERT: B 652 ARG cc_start: 0.6996 (mmt180) cc_final: 0.5784 (mtm110) REVERT: B 814 ASP cc_start: 0.7800 (m-30) cc_final: 0.7289 (m-30) outliers start: 25 outliers final: 11 residues processed: 162 average time/residue: 1.0609 time to fit residues: 189.4835 Evaluate side-chains 149 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 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 449 ILE Chi-restraints excluded: chain B residue 469 VAL Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 623 LYS 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 73 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 110 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 32 optimal weight: 0.0670 chunk 43 optimal weight: 0.8980 overall best weight: 0.6920 ------------------------------------------------------------------------------- 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 71 GLN B 447 ASN B 779 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11394 Z= 0.162 Angle : 0.494 6.420 15472 Z= 0.263 Chirality : 0.042 0.138 1732 Planarity : 0.003 0.032 1920 Dihedral : 8.663 82.879 1570 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.99 % Allowed : 12.50 % Favored : 85.51 % 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: 0.59 (0.23), residues: 1348 helix: 1.45 (0.21), residues: 608 sheet: 1.41 (0.29), residues: 282 loop : -1.81 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.010 0.001 PHE B 317 TYR 0.012 0.001 TYR A 210 ARG 0.004 0.000 ARG B 821 *********************** 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 172 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8348 (mm) cc_final: 0.7820 (tp) REVERT: A 90 ASN cc_start: 0.7974 (m-40) cc_final: 0.7664 (m-40) REVERT: A 143 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: A 145 ILE cc_start: 0.9024 (mt) cc_final: 0.8772 (mp) REVERT: A 536 TYR cc_start: 0.7477 (m-80) cc_final: 0.6967 (m-80) REVERT: A 540 LYS cc_start: 0.8146 (mttm) cc_final: 0.7888 (mmtt) REVERT: A 554 MET cc_start: 0.7322 (tpp) cc_final: 0.7076 (mmt) REVERT: A 602 TYR cc_start: 0.4158 (OUTLIER) cc_final: 0.2963 (m-80) REVERT: A 613 MET cc_start: 0.7143 (tpt) cc_final: 0.6807 (mmm) REVERT: A 707 ARG cc_start: 0.7752 (tpt-90) cc_final: 0.7365 (mtp180) REVERT: B 71 GLN cc_start: 0.8007 (mm-40) cc_final: 0.7581 (mp-120) REVERT: B 83 ASN cc_start: 0.7691 (p0) cc_final: 0.7457 (p0) REVERT: B 121 ASN cc_start: 0.8500 (p0) cc_final: 0.8001 (p0) REVERT: B 143 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.7678 (mm110) REVERT: B 446 TRP cc_start: 0.6020 (OUTLIER) cc_final: 0.5485 (m100) REVERT: B 536 TYR cc_start: 0.7650 (m-80) cc_final: 0.7390 (m-80) REVERT: B 621 PHE cc_start: 0.8550 (m-80) cc_final: 0.8296 (m-80) REVERT: B 652 ARG cc_start: 0.6975 (mmt180) cc_final: 0.5772 (mtm110) outliers start: 24 outliers final: 10 residues processed: 163 average time/residue: 1.0063 time to fit residues: 180.7640 Evaluate side-chains 155 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.347 ------------------------------------------------------------------------------- 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 602 TYR 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 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 623 LYS Chi-restraints excluded: chain B residue 692 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 116 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 447 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 11394 Z= 0.421 Angle : 0.624 6.908 15472 Z= 0.330 Chirality : 0.047 0.208 1732 Planarity : 0.004 0.056 1920 Dihedral : 9.060 88.211 1570 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.48 % Allowed : 12.42 % Favored : 85.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.21), residues: 612 sheet: 1.48 (0.28), residues: 282 loop : -1.71 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 629 HIS 0.004 0.001 HIS B 229 PHE 0.017 0.002 PHE B 632 TYR 0.019 0.002 TYR A 724 ARG 0.008 0.001 ARG A 821 *********************** 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 174 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.7955 (tp) REVERT: A 90 ASN cc_start: 0.8107 (m-40) cc_final: 0.7811 (m-40) REVERT: A 143 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: A 145 ILE cc_start: 0.9048 (mt) cc_final: 0.8794 (mp) REVERT: A 536 TYR cc_start: 0.7503 (m-80) cc_final: 0.7292 (m-80) REVERT: A 540 LYS cc_start: 0.8246 (mttm) cc_final: 0.7940 (mmtt) REVERT: A 554 MET cc_start: 0.7416 (tpp) cc_final: 0.7109 (mmt) REVERT: A 602 TYR cc_start: 0.4485 (OUTLIER) cc_final: 0.3327 (m-80) REVERT: A 613 MET cc_start: 0.7183 (tpt) cc_final: 0.6796 (mmm) REVERT: A 707 ARG cc_start: 0.7818 (tpt-90) cc_final: 0.7395 (mtp180) REVERT: B 276 PHE cc_start: 0.5993 (OUTLIER) cc_final: 0.5157 (t80) REVERT: B 446 TRP cc_start: 0.6072 (OUTLIER) cc_final: 0.5525 (m100) REVERT: B 536 TYR cc_start: 0.7727 (m-80) cc_final: 0.7437 (m-80) REVERT: B 621 PHE cc_start: 0.8475 (m-80) cc_final: 0.8167 (m-80) REVERT: B 652 ARG cc_start: 0.7177 (mmt180) cc_final: 0.6788 (mpt180) outliers start: 30 outliers final: 15 residues processed: 162 average time/residue: 1.0133 time to fit residues: 181.0593 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 : 1.226 ------------------------------------------------------------------------------- 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 155 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR 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 469 VAL Chi-restraints excluded: chain B residue 478 ILE Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 623 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 14 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 GLN B 117 GLN B 447 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 0.052 11394 Z= 0.236 Angle : 0.531 6.328 15472 Z= 0.283 Chirality : 0.043 0.162 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.697 84.426 1570 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.90 % Allowed : 13.41 % Favored : 84.69 % 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: 0.61 (0.23), residues: 1348 helix: 1.31 (0.21), residues: 618 sheet: 1.47 (0.28), residues: 286 loop : -1.69 (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 B 594 PHE 0.015 0.001 PHE B 632 TYR 0.014 0.002 TYR A 188 ARG 0.003 0.000 ARG B 44 *********************** 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 164 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7880 (tp) REVERT: A 90 ASN cc_start: 0.8065 (m-40) cc_final: 0.7787 (m-40) REVERT: A 143 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.7972 (mt0) REVERT: A 145 ILE cc_start: 0.9031 (mt) cc_final: 0.8781 (mp) REVERT: A 536 TYR cc_start: 0.7419 (m-80) cc_final: 0.6902 (m-80) REVERT: A 540 LYS cc_start: 0.8209 (mttm) cc_final: 0.7946 (mmtt) REVERT: A 554 MET cc_start: 0.7305 (tpp) cc_final: 0.7028 (mmt) REVERT: A 602 TYR cc_start: 0.4610 (OUTLIER) cc_final: 0.3280 (m-80) REVERT: A 613 MET cc_start: 0.7171 (tpt) cc_final: 0.6816 (mmm) REVERT: A 707 ARG cc_start: 0.7788 (tpt-90) cc_final: 0.7427 (mtp180) REVERT: B 71 GLN cc_start: 0.7999 (mm-40) cc_final: 0.7506 (mp-120) REVERT: B 83 ASN cc_start: 0.7816 (p0) cc_final: 0.7507 (p0) REVERT: B 276 PHE cc_start: 0.5812 (OUTLIER) cc_final: 0.5016 (t80) REVERT: B 446 TRP cc_start: 0.6084 (OUTLIER) cc_final: 0.5569 (m100) REVERT: B 447 ASN cc_start: 0.7130 (m-40) cc_final: 0.6892 (m-40) REVERT: B 536 TYR cc_start: 0.7575 (m-80) cc_final: 0.7288 (m-80) REVERT: B 621 PHE cc_start: 0.8455 (m-80) cc_final: 0.8126 (m-80) REVERT: B 652 ARG cc_start: 0.6973 (mmt180) cc_final: 0.6569 (mpt180) outliers start: 23 outliers final: 15 residues processed: 157 average time/residue: 1.0271 time to fit residues: 177.5398 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 : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 610 VAL 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 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 478 ILE Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain B residue 666 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11394 Z= 0.239 Angle : 0.541 7.816 15472 Z= 0.286 Chirality : 0.043 0.155 1732 Planarity : 0.003 0.033 1920 Dihedral : 8.543 83.309 1570 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.07 % Allowed : 13.58 % 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: 0.67 (0.23), residues: 1348 helix: 1.42 (0.21), residues: 612 sheet: 1.47 (0.28), residues: 286 loop : -1.68 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 629 HIS 0.003 0.001 HIS B 594 PHE 0.014 0.001 PHE B 632 TYR 0.014 0.002 TYR A 188 ARG 0.006 0.000 ARG A 118 *********************** 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: 25 poor density : 142 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8374 (OUTLIER) cc_final: 0.7797 (tp) REVERT: A 90 ASN cc_start: 0.8038 (m-40) cc_final: 0.7779 (m-40) REVERT: A 143 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.7983 (mt0) REVERT: A 145 ILE cc_start: 0.9045 (mt) cc_final: 0.8801 (mp) REVERT: A 536 TYR cc_start: 0.7454 (m-80) cc_final: 0.6934 (m-80) REVERT: A 540 LYS cc_start: 0.8196 (mttm) cc_final: 0.7917 (mmtt) REVERT: A 554 MET cc_start: 0.7279 (tpp) cc_final: 0.7021 (mmt) REVERT: A 602 TYR cc_start: 0.4602 (OUTLIER) cc_final: 0.3581 (m-80) REVERT: A 613 MET cc_start: 0.7174 (tpt) cc_final: 0.6823 (mmm) REVERT: A 707 ARG cc_start: 0.7767 (tpt-90) cc_final: 0.7409 (mtp180) REVERT: B 83 ASN cc_start: 0.7843 (p0) cc_final: 0.7513 (p0) REVERT: B 133 GLU cc_start: 0.7165 (tt0) cc_final: 0.6681 (tt0) REVERT: B 221 MET cc_start: 0.7243 (mmm) cc_final: 0.6571 (mpm) REVERT: B 276 PHE cc_start: 0.5877 (OUTLIER) cc_final: 0.5045 (t80) REVERT: B 446 TRP cc_start: 0.6005 (OUTLIER) cc_final: 0.5482 (m100) REVERT: B 447 ASN cc_start: 0.7227 (m-40) cc_final: 0.6913 (m110) REVERT: B 536 TYR cc_start: 0.7448 (m-80) cc_final: 0.7211 (m-80) REVERT: B 621 PHE cc_start: 0.8422 (m-80) cc_final: 0.8168 (m-80) REVERT: B 652 ARG cc_start: 0.6980 (mmt180) cc_final: 0.6586 (mpt180) outliers start: 25 outliers final: 14 residues processed: 162 average time/residue: 1.0080 time to fit residues: 180.8318 Evaluate side-chains 156 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 137 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 602 TYR Chi-restraints excluded: chain A residue 610 VAL 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 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 478 ILE Chi-restraints excluded: chain B residue 613 MET Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain B residue 666 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 120 optimal weight: 20.0000 chunk 123 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.0570 chunk 94 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 chunk 113 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 overall best weight: 1.7902 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11394 Z= 0.289 Angle : 0.563 7.088 15472 Z= 0.298 Chirality : 0.045 0.173 1732 Planarity : 0.004 0.036 1920 Dihedral : 8.596 84.771 1570 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.99 % Allowed : 13.66 % 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: 0.68 (0.23), residues: 1348 helix: 1.32 (0.21), residues: 618 sheet: 1.55 (0.28), residues: 282 loop : -1.56 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 629 HIS 0.003 0.001 HIS B 229 PHE 0.015 0.002 PHE B 632 TYR 0.015 0.002 TYR A 188 ARG 0.006 0.000 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2696 Ramachandran restraints generated. 1348 Oldfield, 0 Emsley, 1348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7813 (tp) REVERT: A 90 ASN cc_start: 0.7979 (m-40) cc_final: 0.7727 (m-40) REVERT: A 143 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.7958 (mt0) REVERT: A 145 ILE cc_start: 0.9042 (mt) cc_final: 0.8793 (mp) REVERT: A 478 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7812 (mt) REVERT: A 536 TYR cc_start: 0.7414 (m-80) cc_final: 0.6887 (m-80) REVERT: A 540 LYS cc_start: 0.8208 (mttm) cc_final: 0.7954 (mmmt) REVERT: A 554 MET cc_start: 0.7318 (tpp) cc_final: 0.7049 (mmt) REVERT: A 613 MET cc_start: 0.7171 (tpt) cc_final: 0.6812 (mmm) REVERT: A 707 ARG cc_start: 0.7804 (tpt-90) cc_final: 0.7407 (mtp180) REVERT: B 71 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7569 (mp-120) REVERT: B 83 ASN cc_start: 0.7841 (p0) cc_final: 0.7492 (p0) REVERT: B 133 GLU cc_start: 0.7137 (tt0) cc_final: 0.6672 (tt0) REVERT: B 276 PHE cc_start: 0.5937 (OUTLIER) cc_final: 0.5116 (t80) REVERT: B 446 TRP cc_start: 0.6045 (OUTLIER) cc_final: 0.5559 (m100) REVERT: B 536 TYR cc_start: 0.7436 (m-80) cc_final: 0.7207 (m-80) REVERT: B 621 PHE cc_start: 0.8442 (m-80) cc_final: 0.8168 (m-80) REVERT: B 652 ARG cc_start: 0.7027 (mmt180) cc_final: 0.6614 (mpt180) outliers start: 24 outliers final: 15 residues processed: 154 average time/residue: 1.0044 time to fit residues: 170.6040 Evaluate side-chains 154 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 478 ILE 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 617 LEU 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 478 ILE Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain B residue 666 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 77 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 122 optimal weight: 7.9990 chunk 106 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 0.0030 chunk 113 optimal weight: 2.9990 overall best weight: 1.0594 ------------------------------------------------------------------------------- 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 B 447 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11394 Z= 0.206 Angle : 0.531 8.208 15472 Z= 0.280 Chirality : 0.043 0.150 1732 Planarity : 0.003 0.034 1920 Dihedral : 8.387 82.060 1570 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.74 % Allowed : 13.91 % 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: 0.71 (0.23), residues: 1348 helix: 1.41 (0.21), residues: 618 sheet: 1.47 (0.28), residues: 282 loop : -1.60 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 629 HIS 0.003 0.001 HIS B 594 PHE 0.014 0.001 PHE B 632 TYR 0.014 0.001 TYR A 188 ARG 0.007 0.000 ARG A 118 ********************** 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 156 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: A 44 ARG cc_start: 0.6825 (ttp-170) cc_final: 0.6440 (ptm160) REVERT: A 63 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.7697 (tp) REVERT: A 90 ASN cc_start: 0.7967 (m-40) cc_final: 0.7721 (m-40) REVERT: A 143 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7965 (mt0) REVERT: A 145 ILE cc_start: 0.9034 (mt) cc_final: 0.8789 (mp) REVERT: A 478 ILE cc_start: 0.8052 (OUTLIER) cc_final: 0.7791 (mt) REVERT: A 536 TYR cc_start: 0.7395 (m-80) cc_final: 0.6895 (m-80) REVERT: A 540 LYS cc_start: 0.8134 (mttm) cc_final: 0.7883 (mmtt) REVERT: A 554 MET cc_start: 0.7178 (tpp) cc_final: 0.6959 (mmt) REVERT: A 602 TYR cc_start: 0.4849 (OUTLIER) cc_final: 0.4382 (t80) REVERT: A 613 MET cc_start: 0.7163 (tpt) cc_final: 0.6851 (mmm) REVERT: A 707 ARG cc_start: 0.7756 (tpt-90) cc_final: 0.7401 (mtp180) REVERT: B 83 ASN cc_start: 0.7731 (p0) cc_final: 0.7457 (p0) REVERT: B 133 GLU cc_start: 0.7190 (tt0) cc_final: 0.6726 (tt0) REVERT: B 221 MET cc_start: 0.7170 (mmm) cc_final: 0.6499 (mpm) REVERT: B 276 PHE cc_start: 0.5731 (OUTLIER) cc_final: 0.4840 (t80) REVERT: B 446 TRP cc_start: 0.6045 (OUTLIER) cc_final: 0.5471 (m100) REVERT: B 536 TYR cc_start: 0.7372 (m-80) cc_final: 0.7162 (m-80) REVERT: B 621 PHE cc_start: 0.8413 (m-80) cc_final: 0.8182 (m-80) REVERT: B 652 ARG cc_start: 0.6931 (mmt180) cc_final: 0.6541 (mpt180) outliers start: 21 outliers final: 13 residues processed: 149 average time/residue: 1.0158 time to fit residues: 166.7736 Evaluate side-chains 150 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain A residue 143 GLN Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 478 ILE 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 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 478 ILE Chi-restraints excluded: chain B residue 623 LYS Chi-restraints excluded: chain B residue 666 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 134 random chunks: chunk 32 optimal weight: 6.9990 chunk 98 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.159750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.110500 restraints weight = 12895.520| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.23 r_work: 0.3409 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11394 Z= 0.170 Angle : 0.508 6.338 15472 Z= 0.268 Chirality : 0.043 0.217 1732 Planarity : 0.003 0.033 1920 Dihedral : 8.393 84.585 1570 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.57 % Allowed : 14.24 % 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: 0.90 (0.23), residues: 1348 helix: 1.62 (0.21), residues: 610 sheet: 1.52 (0.28), residues: 282 loop : -1.49 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 629 HIS 0.004 0.001 HIS B 594 PHE 0.012 0.001 PHE B 632 TYR 0.013 0.001 TYR A 210 ARG 0.007 0.000 ARG A 118 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3813.44 seconds wall clock time: 69 minutes 17.22 seconds (4157.22 seconds total)