Starting phenix.real_space_refine on Thu Mar 13 23:22:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rz8_19606/03_2025/8rz8_19606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rz8_19606/03_2025/8rz8_19606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rz8_19606/03_2025/8rz8_19606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rz8_19606/03_2025/8rz8_19606.map" model { file = "/net/cci-nas-00/data/ceres_data/8rz8_19606/03_2025/8rz8_19606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rz8_19606/03_2025/8rz8_19606.cif" } resolution = 3.06 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= 0.001 sd= 0.020 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 P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 5874 2.51 5 N 1585 2.21 5 O 1740 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9255 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4726 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 603, 4723 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 19, 'TRANS': 583} Chain breaks: 11 Conformer: "B" Number of residues, atoms: 603, 4723 Classifications: {'peptide': 603} Link IDs: {'PTRANS': 19, 'TRANS': 583} Chain breaks: 11 bond proxies already assigned to first conformer: 4780 Chain: "B" Number of atoms: 4465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4465 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 17, 'TRANS': 539} Chain breaks: 3 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N SER A 185 " occ=0.00 ... (4 atoms not shown) pdb=" OG SER A 185 " occ=0.00 residue: pdb=" N THR A 234 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 234 " occ=0.00 residue: pdb=" N TYR A 570 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR A 570 " occ=0.00 residue: pdb=" N GLU B 701 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU B 701 " occ=0.00 residue: pdb=" N ILE B 754 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE B 754 " occ=0.00 residue: pdb=" N TYR B1106 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR B1106 " occ=0.00 Time building chain proxies: 8.14, per 1000 atoms: 0.88 Number of scatterers: 9255 At special positions: 0 Unit cell: (81.3638, 107.876, 154.5, 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) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1740 8.00 N 1585 7.00 C 5874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.43 Conformation dependent library (CDL) restraints added in 1.5 seconds 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2200 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 59.0% alpha, 6.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 186 through 195 Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.794A pdb=" N GLY A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 232 Processing helix chain 'A' and resid 236 through 244 removed outlier: 3.573A pdb=" N ARG A 243 " --> pdb=" O GLN A 239 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 282 through 286 Processing helix chain 'A' and resid 303 through 310 Processing helix chain 'A' and resid 325 through 331 Processing helix chain 'A' and resid 335 through 348 removed outlier: 3.513A pdb=" N GLN A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 340 " --> pdb=" O PRO A 336 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU A 341 " --> pdb=" O GLN A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 369 removed outlier: 3.675A pdb=" N ILE A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 386 through 396 Processing helix chain 'A' and resid 400 through 413 removed outlier: 3.542A pdb=" N CYS A 404 " --> pdb=" O ASN A 400 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN A 413 " --> pdb=" O GLN A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 Processing helix chain 'A' and resid 429 through 447 Proline residue: A 439 - end of helix Processing helix chain 'A' and resid 447 through 457 Processing helix chain 'A' and resid 475 through 499 removed outlier: 3.751A pdb=" N GLU A 483 " --> pdb=" O SER A 479 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 484 " --> pdb=" O GLU A 480 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 587 removed outlier: 3.640A pdb=" N THR A 557 " --> pdb=" O ASN A 553 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ASN A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL A 578 " --> pdb=" O GLN A 574 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS A 579 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU A 580 " --> pdb=" O ALA A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 613 Processing helix chain 'A' and resid 674 through 692 removed outlier: 3.557A pdb=" N GLY A 683 " --> pdb=" O ILE A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 755 through 773 Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 789 through 794 removed outlier: 3.927A pdb=" N GLN A 793 " --> pdb=" O ALA A 789 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 834 removed outlier: 3.635A pdb=" N VAL A 830 " --> pdb=" O PHE A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 837 through 851 Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 570 through 582 Processing helix chain 'B' and resid 586 through 603 removed outlier: 3.707A pdb=" N ILE B 590 " --> pdb=" O LYS B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 618 removed outlier: 3.641A pdb=" N ARG B 616 " --> pdb=" O GLU B 612 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N LYS B 617 " --> pdb=" O ASN B 613 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 631 Processing helix chain 'B' and resid 634 through 654 Processing helix chain 'B' and resid 655 through 663 Processing helix chain 'B' and resid 665 through 673 Processing helix chain 'B' and resid 674 through 679 removed outlier: 3.550A pdb=" N LEU B 678 " --> pdb=" O GLU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 680 through 682 No H-bonds generated for 'chain 'B' and resid 680 through 682' Processing helix chain 'B' and resid 683 through 688 Processing helix chain 'B' and resid 690 through 697 removed outlier: 3.782A pdb=" N VAL B 696 " --> pdb=" O GLN B 692 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY B 697 " --> pdb=" O ALA B 693 " (cutoff:3.500A) Processing helix chain 'B' and resid 709 through 729 removed outlier: 3.761A pdb=" N LYS B 713 " --> pdb=" O PHE B 709 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N HIS B 729 " --> pdb=" O GLU B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 737 removed outlier: 3.562A pdb=" N ILE B 733 " --> pdb=" O HIS B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 782 through 815 Processing helix chain 'B' and resid 817 through 843 Processing helix chain 'B' and resid 864 through 871 Processing helix chain 'B' and resid 901 through 919 removed outlier: 3.975A pdb=" N THR B 913 " --> pdb=" O VAL B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 965 Processing helix chain 'B' and resid 982 through 1000 Processing helix chain 'B' and resid 1011 through 1016 Processing helix chain 'B' and resid 1017 through 1021 removed outlier: 3.593A pdb=" N ASN B1020 " --> pdb=" O LEU B1017 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1076 removed outlier: 3.784A pdb=" N VAL B1072 " --> pdb=" O TYR B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1079 through 1108 Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 151 Processing sheet with id=AA2, first strand: chain 'A' and resid 653 through 657 removed outlier: 4.812A pdb=" N ASN A 653 " --> pdb=" O ALA A 636 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A 636 " --> pdb=" O ASN A 653 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER A 699 " --> pdb=" O LYS A 635 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 707 through 711 removed outlier: 3.924A pdb=" N ILE A 747 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LYS A 818 " --> pdb=" O HIS A 801 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 756 through 757 Processing sheet with id=AA5, first strand: chain 'B' and resid 880 through 885 removed outlier: 4.766A pdb=" N ASN B 880 " --> pdb=" O ASN B 861 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASN B 861 " --> pdb=" O ASN B 880 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU B 926 " --> pdb=" O LYS B 860 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 935 through 938 removed outlier: 6.407A pdb=" N PHE B 936 " --> pdb=" O ILE B 973 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N ASP B 975 " --> pdb=" O PHE B 936 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ARG B 938 " --> pdb=" O ASP B 975 " (cutoff:3.500A) 500 hydrogen bonds defined for protein. 1463 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: 2.65 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.30: 1546 1.30 - 1.46: 3394 1.46 - 1.62: 4387 1.62 - 1.78: 0 1.78 - 1.94: 74 Bond restraints: 9401 Sorted by residual: bond pdb=" CG ASN B1071 " pdb=" OD1 ASN B1071 " ideal model delta sigma weight residual 1.231 1.140 0.091 1.90e-02 2.77e+03 2.31e+01 bond pdb=" O2G AGS B2001 " pdb=" PG AGS B2001 " ideal model delta sigma weight residual 1.557 1.501 0.056 2.00e-02 2.50e+03 7.93e+00 bond pdb=" CA SER B 570 " pdb=" CB SER B 570 " ideal model delta sigma weight residual 1.533 1.490 0.043 1.58e-02 4.01e+03 7.55e+00 bond pdb=" O3G AGS A2001 " pdb=" PG AGS A2001 " ideal model delta sigma weight residual 1.558 1.503 0.055 2.00e-02 2.50e+03 7.45e+00 bond pdb=" O2A AGS B2001 " pdb=" PA AGS B2001 " ideal model delta sigma weight residual 1.531 1.488 0.043 1.60e-02 3.91e+03 7.34e+00 ... (remaining 9396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 12083 2.30 - 4.60: 566 4.60 - 6.89: 32 6.89 - 9.19: 8 9.19 - 11.49: 5 Bond angle restraints: 12694 Sorted by residual: angle pdb=" OD1 ASN B1071 " pdb=" CG ASN B1071 " pdb=" ND2 ASN B1071 " ideal model delta sigma weight residual 122.60 113.16 9.44 1.00e+00 1.00e+00 8.91e+01 angle pdb=" CA PHE A 450 " pdb=" CB PHE A 450 " pdb=" CG PHE A 450 " ideal model delta sigma weight residual 113.80 118.53 -4.73 1.00e+00 1.00e+00 2.24e+01 angle pdb=" N ILE B 675 " pdb=" CA ILE B 675 " pdb=" CB ILE B 675 " ideal model delta sigma weight residual 110.45 113.76 -3.31 7.80e-01 1.64e+00 1.80e+01 angle pdb=" CA ASP A 597 " pdb=" CB ASP A 597 " pdb=" CG ASP A 597 " ideal model delta sigma weight residual 112.60 116.76 -4.16 1.00e+00 1.00e+00 1.73e+01 angle pdb=" CB ASN B1071 " pdb=" CG ASN B1071 " pdb=" OD1 ASN B1071 " ideal model delta sigma weight residual 120.80 128.92 -8.12 2.00e+00 2.50e-01 1.65e+01 ... (remaining 12689 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 4986 17.75 - 35.50: 585 35.50 - 53.25: 124 53.25 - 70.99: 40 70.99 - 88.74: 14 Dihedral angle restraints: 5749 sinusoidal: 2369 harmonic: 3380 Sorted by residual: dihedral pdb=" CA THR A 812 " pdb=" C THR A 812 " pdb=" N MET A 813 " pdb=" CA MET A 813 " ideal model delta harmonic sigma weight residual -180.00 -159.54 -20.46 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA ASP A 379 " pdb=" C ASP A 379 " pdb=" N LEU A 380 " pdb=" CA LEU A 380 " ideal model delta harmonic sigma weight residual -180.00 -160.52 -19.48 0 5.00e+00 4.00e-02 1.52e+01 dihedral pdb=" CA ARG B 890 " pdb=" C ARG B 890 " pdb=" N VAL B 891 " pdb=" CA VAL B 891 " ideal model delta harmonic sigma weight residual -180.00 -162.40 -17.60 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 5746 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 755 0.057 - 0.114: 492 0.114 - 0.171: 184 0.171 - 0.228: 36 0.228 - 0.285: 12 Chirality restraints: 1479 Sorted by residual: chirality pdb=" CA ASP A 597 " pdb=" N ASP A 597 " pdb=" C ASP A 597 " pdb=" CB ASP A 597 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA GLN A 451 " pdb=" N GLN A 451 " pdb=" C GLN A 451 " pdb=" CB GLN A 451 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.29 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" CA ASN A 354 " pdb=" N ASN A 354 " pdb=" C ASN A 354 " pdb=" CB ASN A 354 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 1476 not shown) Planarity restraints: 1600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 438 " -0.030 5.00e-02 4.00e+02 4.55e-02 3.31e+00 pdb=" N PRO A 439 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 439 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 439 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 438 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C THR A 438 " 0.030 2.00e-02 2.50e+03 pdb=" O THR A 438 " -0.011 2.00e-02 2.50e+03 pdb=" N PRO A 439 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 415 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C PRO A 415 " 0.022 2.00e-02 2.50e+03 pdb=" O PRO A 415 " -0.008 2.00e-02 2.50e+03 pdb=" N ASN A 416 " -0.008 2.00e-02 2.50e+03 ... (remaining 1597 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 14 2.36 - 3.00: 4862 3.00 - 3.63: 14709 3.63 - 4.27: 21712 4.27 - 4.90: 35946 Nonbonded interactions: 77243 Sorted by model distance: nonbonded pdb=" OG SER B 903 " pdb="MG MG B2000 " model vdw 1.729 2.170 nonbonded pdb=" OG SER A 676 " pdb="MG MG A2000 " model vdw 2.004 2.170 nonbonded pdb=" OD1 ASN B 660 " pdb=" NH2 ARG B 669 " model vdw 2.059 3.120 nonbonded pdb="MG MG A2000 " pdb=" O2G AGS A2001 " model vdw 2.085 2.170 nonbonded pdb=" OE2 GLU B 889 " pdb=" OH TYR B1028 " model vdw 2.129 3.040 ... (remaining 77238 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.90 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: 2.120 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.640 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 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 0.091 9401 Z= 0.450 Angle : 1.186 11.490 12694 Z= 0.785 Chirality : 0.082 0.285 1479 Planarity : 0.004 0.046 1600 Dihedral : 16.614 88.743 3549 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.74 % Allowed : 18.51 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.24), residues: 1129 helix: 0.21 (0.20), residues: 616 sheet: -1.30 (0.55), residues: 93 loop : -1.86 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP B 579 HIS 0.008 0.002 HIS B 729 PHE 0.012 0.003 PHE A 474 TYR 0.016 0.003 TYR B1011 ARG 0.016 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 251 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 635 LYS cc_start: 0.8272 (mptt) cc_final: 0.8030 (mptt) REVERT: A 722 VAL cc_start: 0.7570 (t) cc_final: 0.7265 (m) REVERT: A 743 SER cc_start: 0.8244 (t) cc_final: 0.7888 (m) REVERT: A 802 VAL cc_start: 0.8477 (t) cc_final: 0.8253 (m) REVERT: A 814 LEU cc_start: 0.8169 (mt) cc_final: 0.7941 (mm) REVERT: B 554 MET cc_start: 0.7787 (mmm) cc_final: 0.7562 (mmm) REVERT: B 587 LEU cc_start: 0.8299 (tp) cc_final: 0.7578 (tp) REVERT: B 591 ASN cc_start: 0.7650 (m-40) cc_final: 0.7385 (m-40) outliers start: 28 outliers final: 13 residues processed: 268 average time/residue: 0.2859 time to fit residues: 98.8736 Evaluate side-chains 251 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 238 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 654 ASP Chi-restraints excluded: chain A residue 806 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 730 LEU Chi-restraints excluded: chain B residue 764 ILE Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 871 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 46 optimal weight: 0.8980 chunk 90 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 67 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 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 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B1058 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.153534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.127645 restraints weight = 22637.494| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 3.17 r_work: 0.3621 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 956 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3614 r_free = 0.3614 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9401 Z= 0.296 Angle : 0.673 10.244 12694 Z= 0.350 Chirality : 0.044 0.217 1479 Planarity : 0.005 0.061 1600 Dihedral : 6.973 58.926 1294 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.13 % Allowed : 19.98 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.24), residues: 1129 helix: 0.54 (0.20), residues: 629 sheet: -1.35 (0.54), residues: 93 loop : -1.52 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 764 HIS 0.008 0.001 HIS A 424 PHE 0.028 0.002 PHE A 474 TYR 0.018 0.002 TYR A 769 ARG 0.007 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 357 GLU cc_start: 0.7617 (mm-30) cc_final: 0.7085 (mm-30) REVERT: A 480 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8113 (tp30) REVERT: A 613 ASN cc_start: 0.7859 (t0) cc_final: 0.7656 (t0) REVERT: A 617 VAL cc_start: 0.8244 (t) cc_final: 0.7971 (p) REVERT: A 635 LYS cc_start: 0.8283 (mptt) cc_final: 0.7957 (mptt) REVERT: A 722 VAL cc_start: 0.7465 (t) cc_final: 0.7172 (m) REVERT: A 743 SER cc_start: 0.8303 (t) cc_final: 0.7942 (m) REVERT: A 853 GLU cc_start: 0.7206 (pm20) cc_final: 0.6768 (pm20) REVERT: B 549 GLN cc_start: 0.7807 (pt0) cc_final: 0.7276 (pt0) REVERT: B 554 MET cc_start: 0.7424 (mmm) cc_final: 0.6680 (mmm) REVERT: B 587 LEU cc_start: 0.8065 (tp) cc_final: 0.7418 (tp) REVERT: B 591 ASN cc_start: 0.7606 (m-40) cc_final: 0.7333 (m110) REVERT: B 718 GLU cc_start: 0.7870 (pp20) cc_final: 0.7604 (pp20) REVERT: B 902 LYS cc_start: 0.8091 (mtmm) cc_final: 0.7805 (mtmm) REVERT: B 1055 PHE cc_start: 0.7780 (m-80) cc_final: 0.7560 (m-80) outliers start: 32 outliers final: 20 residues processed: 266 average time/residue: 0.2929 time to fit residues: 100.1127 Evaluate side-chains 258 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 238 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 MET Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 599 LEU Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 842 GLU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 GLN Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1053 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 83 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 671 ASN ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 750 GLN B 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.152648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.128682 restraints weight = 15216.543| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.38 r_work: 0.3678 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9401 Z= 0.306 Angle : 0.642 10.381 12694 Z= 0.331 Chirality : 0.043 0.209 1479 Planarity : 0.005 0.059 1600 Dihedral : 6.531 57.455 1281 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 3.33 % Allowed : 21.45 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.24), residues: 1129 helix: 0.58 (0.20), residues: 631 sheet: -1.29 (0.54), residues: 93 loop : -1.41 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 764 HIS 0.009 0.001 HIS A 424 PHE 0.028 0.002 PHE A 474 TYR 0.023 0.002 TYR A 299 ARG 0.006 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 480 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8186 (tp30) REVERT: A 617 VAL cc_start: 0.8307 (t) cc_final: 0.8035 (p) REVERT: A 635 LYS cc_start: 0.8305 (mptt) cc_final: 0.7981 (mptt) REVERT: A 651 ILE cc_start: 0.8674 (mm) cc_final: 0.8413 (mp) REVERT: A 691 ILE cc_start: 0.8041 (tt) cc_final: 0.7783 (pt) REVERT: A 722 VAL cc_start: 0.7591 (t) cc_final: 0.7311 (m) REVERT: A 743 SER cc_start: 0.8412 (t) cc_final: 0.8072 (m) REVERT: A 814 LEU cc_start: 0.8162 (mt) cc_final: 0.7910 (mm) REVERT: B 549 GLN cc_start: 0.7906 (pt0) cc_final: 0.7229 (pt0) REVERT: B 554 MET cc_start: 0.7591 (mmm) cc_final: 0.7127 (mmm) REVERT: B 586 LYS cc_start: 0.7586 (mtmm) cc_final: 0.7347 (mtmm) REVERT: B 591 ASN cc_start: 0.7822 (m-40) cc_final: 0.7600 (m-40) REVERT: B 718 GLU cc_start: 0.7926 (pp20) cc_final: 0.7711 (pp20) REVERT: B 734 ARG cc_start: 0.7165 (ttp80) cc_final: 0.6741 (ttp80) REVERT: B 861 ASN cc_start: 0.8212 (m-40) cc_final: 0.7979 (m-40) REVERT: B 902 LYS cc_start: 0.8234 (mtmm) cc_final: 0.7837 (mtmm) REVERT: B 953 MET cc_start: 0.8153 (tpp) cc_final: 0.7749 (tpp) REVERT: B 972 VAL cc_start: 0.7984 (t) cc_final: 0.7663 (m) outliers start: 34 outliers final: 25 residues processed: 262 average time/residue: 0.2798 time to fit residues: 94.1514 Evaluate side-chains 264 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 573 ARG Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 715 ARG Chi-restraints excluded: chain B residue 781 HIS Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 874 GLN Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1056 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 348 GLN ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.152283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.126056 restraints weight = 22257.317| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 3.10 r_work: 0.3623 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3616 r_free = 0.3616 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9401 Z= 0.331 Angle : 0.650 13.043 12694 Z= 0.331 Chirality : 0.044 0.218 1479 Planarity : 0.005 0.056 1600 Dihedral : 6.455 57.614 1278 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.82 % Allowed : 21.94 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.25), residues: 1129 helix: 0.51 (0.20), residues: 638 sheet: -1.26 (0.55), residues: 93 loop : -1.38 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 764 HIS 0.009 0.001 HIS A 424 PHE 0.027 0.002 PHE A 474 TYR 0.030 0.002 TYR A 299 ARG 0.008 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 241 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 304 ILE cc_start: 0.8511 (mm) cc_final: 0.8233 (mm) REVERT: A 357 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 384 PHE cc_start: 0.7571 (OUTLIER) cc_final: 0.7102 (m-80) REVERT: A 480 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8160 (tp30) REVERT: A 617 VAL cc_start: 0.8245 (t) cc_final: 0.7978 (p) REVERT: A 635 LYS cc_start: 0.8205 (mptt) cc_final: 0.7833 (mptt) REVERT: A 651 ILE cc_start: 0.8687 (mm) cc_final: 0.8445 (mp) REVERT: A 722 VAL cc_start: 0.7570 (t) cc_final: 0.7333 (m) REVERT: A 743 SER cc_start: 0.8290 (t) cc_final: 0.7978 (m) REVERT: A 814 LEU cc_start: 0.8135 (mt) cc_final: 0.7885 (mm) REVERT: B 549 GLN cc_start: 0.7804 (pt0) cc_final: 0.7553 (pt0) REVERT: B 591 ASN cc_start: 0.7680 (m-40) cc_final: 0.7447 (m-40) REVERT: B 734 ARG cc_start: 0.7115 (ttp80) cc_final: 0.6809 (ttp80) REVERT: B 861 ASN cc_start: 0.8127 (m-40) cc_final: 0.7880 (m-40) REVERT: B 953 MET cc_start: 0.8048 (tpp) cc_final: 0.7835 (tpt) REVERT: B 972 VAL cc_start: 0.7824 (t) cc_final: 0.7486 (m) outliers start: 39 outliers final: 32 residues processed: 260 average time/residue: 0.3075 time to fit residues: 102.3991 Evaluate side-chains 274 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 400 ASN Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 643 GLU Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 573 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 715 ARG Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1053 VAL Chi-restraints excluded: chain B residue 1056 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 38 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 544 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1058 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.153235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.129130 restraints weight = 15032.768| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.36 r_work: 0.3689 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3536 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3536 r_free = 0.3536 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3536 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9401 Z= 0.291 Angle : 0.630 11.150 12694 Z= 0.323 Chirality : 0.044 0.278 1479 Planarity : 0.005 0.053 1600 Dihedral : 6.488 56.871 1278 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.62 % Allowed : 23.02 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.25), residues: 1129 helix: 0.62 (0.20), residues: 631 sheet: -0.96 (0.59), residues: 83 loop : -1.36 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 764 HIS 0.009 0.001 HIS A 424 PHE 0.028 0.002 PHE A 474 TYR 0.031 0.002 TYR A 299 ARG 0.008 0.001 ARG A 631 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 247 time to evaluate : 1.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 LEU cc_start: 0.8663 (mp) cc_final: 0.8421 (mp) REVERT: A 384 PHE cc_start: 0.7668 (OUTLIER) cc_final: 0.7197 (m-80) REVERT: A 414 LEU cc_start: 0.7051 (OUTLIER) cc_final: 0.6739 (mt) REVERT: A 422 GLU cc_start: 0.8080 (tp30) cc_final: 0.6886 (tp30) REVERT: A 617 VAL cc_start: 0.8294 (t) cc_final: 0.8029 (p) REVERT: A 651 ILE cc_start: 0.8707 (mm) cc_final: 0.8459 (mp) REVERT: A 690 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7802 (mt0) REVERT: A 722 VAL cc_start: 0.7593 (t) cc_final: 0.7348 (m) REVERT: A 743 SER cc_start: 0.8409 (t) cc_final: 0.8084 (m) REVERT: A 814 LEU cc_start: 0.8223 (mt) cc_final: 0.7965 (mm) REVERT: B 591 ASN cc_start: 0.7828 (m-40) cc_final: 0.7602 (m110) REVERT: B 690 ASN cc_start: 0.8020 (t0) cc_final: 0.7459 (t0) REVERT: B 702 LEU cc_start: 0.4974 (OUTLIER) cc_final: 0.4715 (mm) REVERT: B 793 ASN cc_start: 0.8298 (m-40) cc_final: 0.8066 (m110) REVERT: B 972 VAL cc_start: 0.7996 (t) cc_final: 0.7665 (m) outliers start: 37 outliers final: 27 residues processed: 269 average time/residue: 0.3043 time to fit residues: 105.2519 Evaluate side-chains 266 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 573 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 715 ARG Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1005 THR Chi-restraints excluded: chain B residue 1056 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 103 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 100 optimal weight: 0.5980 chunk 32 optimal weight: 0.0270 chunk 59 optimal weight: 0.0470 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 0.0570 chunk 1 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 15 optimal weight: 0.0870 overall best weight: 0.1032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 613 ASN ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN A 799 ASN B 544 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.157181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.133009 restraints weight = 15434.673| |-----------------------------------------------------------------------------| r_work (start): 0.3854 rms_B_bonded: 2.43 r_work: 0.3744 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3734 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3734 r_free = 0.3734 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3734 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9401 Z= 0.170 Angle : 0.593 10.699 12694 Z= 0.300 Chirality : 0.041 0.205 1479 Planarity : 0.004 0.048 1600 Dihedral : 6.281 54.411 1278 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.72 % Allowed : 23.51 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1129 helix: 0.87 (0.20), residues: 636 sheet: -1.07 (0.55), residues: 93 loop : -1.26 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 807 HIS 0.009 0.001 HIS A 424 PHE 0.019 0.001 PHE B 936 TYR 0.018 0.001 TYR A 299 ARG 0.008 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 233 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 TYR cc_start: 0.7753 (m-10) cc_final: 0.7490 (m-80) REVERT: A 384 PHE cc_start: 0.7324 (OUTLIER) cc_final: 0.6867 (m-80) REVERT: A 414 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6488 (mt) REVERT: A 617 VAL cc_start: 0.8142 (t) cc_final: 0.7887 (p) REVERT: A 651 ILE cc_start: 0.8570 (mm) cc_final: 0.8311 (mp) REVERT: A 690 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.7415 (mp10) REVERT: A 722 VAL cc_start: 0.7424 (t) cc_final: 0.7167 (m) REVERT: A 743 SER cc_start: 0.8190 (t) cc_final: 0.7831 (m) REVERT: A 811 LEU cc_start: 0.7363 (mp) cc_final: 0.7125 (mp) REVERT: A 814 LEU cc_start: 0.7991 (mt) cc_final: 0.7737 (mm) REVERT: B 584 LEU cc_start: 0.8436 (mm) cc_final: 0.8179 (mt) REVERT: B 589 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7642 (mt-10) REVERT: B 591 ASN cc_start: 0.7492 (m-40) cc_final: 0.7219 (m110) REVERT: B 593 ARG cc_start: 0.8134 (tpp80) cc_final: 0.7911 (ttm170) REVERT: B 861 ASN cc_start: 0.7958 (m110) cc_final: 0.7753 (m-40) REVERT: B 902 LYS cc_start: 0.8076 (mtmm) cc_final: 0.7805 (mtmm) REVERT: B 936 PHE cc_start: 0.7231 (m-80) cc_final: 0.6823 (m-10) REVERT: B 944 ASN cc_start: 0.7904 (t0) cc_final: 0.7605 (t0) REVERT: B 972 VAL cc_start: 0.7727 (t) cc_final: 0.7360 (m) outliers start: 38 outliers final: 27 residues processed: 258 average time/residue: 0.3038 time to fit residues: 101.0425 Evaluate side-chains 260 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 230 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 613 ASN Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 573 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 715 ARG Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 56 optimal weight: 0.3980 chunk 37 optimal weight: 0.0040 chunk 19 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 0.6980 chunk 3 optimal weight: 9.9990 chunk 113 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.155816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.131688 restraints weight = 15081.224| |-----------------------------------------------------------------------------| r_work (start): 0.3840 rms_B_bonded: 2.38 r_work: 0.3730 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3570 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3550 r_free = 0.3550 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9401 Z= 0.243 Angle : 0.611 9.486 12694 Z= 0.310 Chirality : 0.043 0.225 1479 Planarity : 0.004 0.051 1600 Dihedral : 6.045 56.721 1276 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.72 % Allowed : 23.41 % Favored : 72.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1129 helix: 0.84 (0.20), residues: 637 sheet: -0.66 (0.58), residues: 86 loop : -1.28 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 764 HIS 0.008 0.001 HIS A 424 PHE 0.029 0.002 PHE A 760 TYR 0.022 0.001 TYR A 299 ARG 0.008 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 TYR cc_start: 0.7949 (m-10) cc_final: 0.7743 (m-80) REVERT: A 384 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7063 (m-80) REVERT: A 414 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6645 (mt) REVERT: A 480 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8101 (tp30) REVERT: A 613 ASN cc_start: 0.7744 (t0) cc_final: 0.7460 (t0) REVERT: A 617 VAL cc_start: 0.8252 (t) cc_final: 0.7991 (p) REVERT: A 651 ILE cc_start: 0.8674 (mm) cc_final: 0.8418 (mp) REVERT: A 675 LYS cc_start: 0.7252 (mttp) cc_final: 0.6933 (mttp) REVERT: A 690 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: A 722 VAL cc_start: 0.7530 (t) cc_final: 0.7264 (m) REVERT: A 743 SER cc_start: 0.8375 (t) cc_final: 0.8018 (m) REVERT: A 811 LEU cc_start: 0.7378 (mp) cc_final: 0.7150 (mp) REVERT: A 814 LEU cc_start: 0.8144 (mt) cc_final: 0.7890 (mm) REVERT: B 649 LYS cc_start: 0.8309 (ttpp) cc_final: 0.7839 (tmtt) REVERT: B 861 ASN cc_start: 0.8121 (m110) cc_final: 0.7905 (m-40) REVERT: B 902 LYS cc_start: 0.8185 (mtmm) cc_final: 0.7906 (mtmm) REVERT: B 944 ASN cc_start: 0.7975 (t0) cc_final: 0.7658 (t0) REVERT: B 1099 THR cc_start: 0.7564 (m) cc_final: 0.7351 (p) outliers start: 38 outliers final: 26 residues processed: 261 average time/residue: 0.2813 time to fit residues: 94.0179 Evaluate side-chains 258 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 229 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 573 ARG Chi-restraints excluded: chain B residue 585 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 715 ARG Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 30 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 98 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 0.0670 chunk 55 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 591 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.155008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.130868 restraints weight = 15118.177| |-----------------------------------------------------------------------------| r_work (start): 0.3810 rms_B_bonded: 2.38 r_work: 0.3700 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3541 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9401 Z= 0.273 Angle : 0.620 10.096 12694 Z= 0.315 Chirality : 0.043 0.229 1479 Planarity : 0.005 0.051 1600 Dihedral : 6.080 58.140 1276 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.23 % Allowed : 24.00 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1129 helix: 0.79 (0.20), residues: 642 sheet: -0.72 (0.59), residues: 85 loop : -1.24 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 764 HIS 0.008 0.001 HIS A 424 PHE 0.026 0.002 PHE A 760 TYR 0.024 0.001 TYR A 299 ARG 0.009 0.001 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 235 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 TYR cc_start: 0.7984 (m-10) cc_final: 0.7774 (m-80) REVERT: A 384 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: A 414 LEU cc_start: 0.6951 (OUTLIER) cc_final: 0.6666 (mt) REVERT: A 422 GLU cc_start: 0.8084 (tp30) cc_final: 0.7032 (mm-30) REVERT: A 449 LYS cc_start: 0.7229 (tppt) cc_final: 0.6994 (tppt) REVERT: A 617 VAL cc_start: 0.8284 (t) cc_final: 0.8014 (p) REVERT: A 651 ILE cc_start: 0.8693 (mm) cc_final: 0.8438 (mp) REVERT: A 675 LYS cc_start: 0.7242 (mttp) cc_final: 0.6929 (mttp) REVERT: A 690 GLN cc_start: 0.8262 (OUTLIER) cc_final: 0.7710 (mp10) REVERT: A 722 VAL cc_start: 0.7558 (t) cc_final: 0.7323 (m) REVERT: A 743 SER cc_start: 0.8381 (t) cc_final: 0.8034 (m) REVERT: A 814 LEU cc_start: 0.8150 (mt) cc_final: 0.7883 (mm) REVERT: B 549 GLN cc_start: 0.7782 (pt0) cc_final: 0.7258 (pt0) REVERT: B 554 MET cc_start: 0.7595 (mmm) cc_final: 0.6986 (mmm) REVERT: B 649 LYS cc_start: 0.8350 (ttpp) cc_final: 0.8130 (ttpp) REVERT: B 861 ASN cc_start: 0.8132 (m110) cc_final: 0.7902 (m-40) REVERT: B 902 LYS cc_start: 0.8243 (mtmm) cc_final: 0.7958 (mtmm) REVERT: B 944 ASN cc_start: 0.7984 (t0) cc_final: 0.7656 (t0) REVERT: B 1099 THR cc_start: 0.7567 (m) cc_final: 0.7358 (p) outliers start: 33 outliers final: 24 residues processed: 256 average time/residue: 0.2880 time to fit residues: 94.6921 Evaluate side-chains 260 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 233 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 737 ARG Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 573 ARG Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 110 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 106 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 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 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 544 ASN B 591 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 917 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.154221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.127999 restraints weight = 22133.159| |-----------------------------------------------------------------------------| r_work (start): 0.3781 rms_B_bonded: 3.07 r_work: 0.3643 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3640 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3640 r_free = 0.3640 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3640 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 9401 Z= 0.310 Angle : 0.635 8.234 12694 Z= 0.327 Chirality : 0.044 0.234 1479 Planarity : 0.005 0.051 1600 Dihedral : 6.133 58.617 1276 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.72 % Allowed : 23.70 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.25), residues: 1129 helix: 0.78 (0.20), residues: 636 sheet: -0.74 (0.59), residues: 85 loop : -1.25 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 764 HIS 0.008 0.001 HIS A 424 PHE 0.025 0.002 PHE A 760 TYR 0.024 0.002 TYR A 299 ARG 0.009 0.001 ARG A 382 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 235 time to evaluate : 1.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.7538 (OUTLIER) cc_final: 0.7034 (m-80) REVERT: A 414 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6630 (mt) REVERT: A 422 GLU cc_start: 0.8047 (tp30) cc_final: 0.6909 (tp30) REVERT: A 431 LEU cc_start: 0.8436 (tp) cc_final: 0.8215 (tt) REVERT: A 449 LYS cc_start: 0.7049 (tppt) cc_final: 0.6798 (tppt) REVERT: A 617 VAL cc_start: 0.8240 (t) cc_final: 0.7977 (p) REVERT: A 651 ILE cc_start: 0.8698 (mm) cc_final: 0.8438 (mp) REVERT: A 675 LYS cc_start: 0.7178 (mttp) cc_final: 0.6865 (mttp) REVERT: A 690 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7572 (mp10) REVERT: A 722 VAL cc_start: 0.7527 (t) cc_final: 0.7298 (m) REVERT: A 743 SER cc_start: 0.8268 (t) cc_final: 0.7932 (m) REVERT: A 814 LEU cc_start: 0.8113 (mt) cc_final: 0.7845 (mm) REVERT: B 549 GLN cc_start: 0.7681 (pt0) cc_final: 0.7104 (pt0) REVERT: B 554 MET cc_start: 0.7399 (mmm) cc_final: 0.6698 (mmm) REVERT: B 649 LYS cc_start: 0.8309 (ttpp) cc_final: 0.8102 (ttpp) REVERT: B 861 ASN cc_start: 0.8008 (m110) cc_final: 0.7784 (m-40) REVERT: B 902 LYS cc_start: 0.8207 (mtmm) cc_final: 0.7902 (mtmm) REVERT: B 944 ASN cc_start: 0.7945 (t0) cc_final: 0.7619 (t0) REVERT: B 972 VAL cc_start: 0.7826 (t) cc_final: 0.7459 (m) outliers start: 38 outliers final: 27 residues processed: 255 average time/residue: 0.2985 time to fit residues: 97.7823 Evaluate side-chains 261 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 838 LYS Chi-restraints excluded: chain B residue 573 ARG Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1003 SER Chi-restraints excluded: chain B residue 1005 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 58 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 78 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 82 optimal weight: 0.4980 chunk 12 optimal weight: 0.2980 chunk 85 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 544 ASN B 591 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 898 ASN B1010 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.154841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.128600 restraints weight = 22274.817| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 3.11 r_work: 0.3651 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3642 r_free = 0.3642 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 9401 Z= 0.262 Angle : 0.626 10.231 12694 Z= 0.320 Chirality : 0.043 0.223 1479 Planarity : 0.005 0.049 1600 Dihedral : 6.112 57.997 1276 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.84 % Allowed : 24.88 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1129 helix: 0.80 (0.20), residues: 637 sheet: -0.71 (0.58), residues: 86 loop : -1.27 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 764 HIS 0.009 0.001 HIS A 424 PHE 0.025 0.002 PHE A 760 TYR 0.022 0.001 TYR A 299 ARG 0.009 0.001 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2258 Ramachandran restraints generated. 1129 Oldfield, 0 Emsley, 1129 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.7514 (OUTLIER) cc_final: 0.7001 (m-80) REVERT: A 414 LEU cc_start: 0.6865 (OUTLIER) cc_final: 0.6613 (mt) REVERT: A 422 GLU cc_start: 0.8045 (tp30) cc_final: 0.6916 (tp30) REVERT: A 431 LEU cc_start: 0.8437 (tp) cc_final: 0.8219 (tt) REVERT: A 449 LYS cc_start: 0.7075 (tppt) cc_final: 0.6873 (tppt) REVERT: A 617 VAL cc_start: 0.8232 (t) cc_final: 0.7967 (p) REVERT: A 651 ILE cc_start: 0.8677 (mm) cc_final: 0.8410 (mp) REVERT: A 675 LYS cc_start: 0.7146 (mttp) cc_final: 0.6832 (mttp) REVERT: A 690 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7491 (mp10) REVERT: A 722 VAL cc_start: 0.7517 (t) cc_final: 0.7295 (m) REVERT: A 743 SER cc_start: 0.8263 (t) cc_final: 0.7915 (m) REVERT: A 814 LEU cc_start: 0.8093 (mt) cc_final: 0.7819 (mm) REVERT: B 549 GLN cc_start: 0.7683 (pt0) cc_final: 0.7202 (pt0) REVERT: B 649 LYS cc_start: 0.8290 (ttpp) cc_final: 0.7992 (tttm) REVERT: B 861 ASN cc_start: 0.8001 (m110) cc_final: 0.7779 (m-40) REVERT: B 902 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7906 (mtmm) REVERT: B 944 ASN cc_start: 0.7947 (t0) cc_final: 0.7620 (t0) REVERT: B 972 VAL cc_start: 0.7841 (t) cc_final: 0.7474 (m) outliers start: 29 outliers final: 24 residues processed: 247 average time/residue: 0.2974 time to fit residues: 93.9101 Evaluate side-chains 253 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 226 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 656 TYR Chi-restraints excluded: chain A residue 690 GLN Chi-restraints excluded: chain A residue 803 THR Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 671 VAL Chi-restraints excluded: chain B residue 673 LEU Chi-restraints excluded: chain B residue 675 ILE Chi-restraints excluded: chain B residue 684 HIS Chi-restraints excluded: chain B residue 702 LEU Chi-restraints excluded: chain B residue 786 VAL Chi-restraints excluded: chain B residue 845 ASP Chi-restraints excluded: chain B residue 850 THR Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 967 THR Chi-restraints excluded: chain B residue 985 ASP Chi-restraints excluded: chain B residue 1003 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 22 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 98 optimal weight: 0.0970 chunk 21 optimal weight: 0.6980 chunk 99 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 89 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN B 591 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.155165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.130254 restraints weight = 17214.935| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.62 r_work: 0.3687 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9401 Z= 0.238 Angle : 0.613 8.640 12694 Z= 0.314 Chirality : 0.043 0.223 1479 Planarity : 0.004 0.049 1600 Dihedral : 6.078 57.939 1276 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.13 % Allowed : 24.58 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1129 helix: 0.81 (0.20), residues: 636 sheet: -0.67 (0.58), residues: 86 loop : -1.24 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 764 HIS 0.009 0.001 HIS A 424 PHE 0.026 0.002 PHE A 760 TYR 0.020 0.001 TYR A 299 ARG 0.009 0.001 ARG A 382 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9581.36 seconds wall clock time: 167 minutes 14.22 seconds (10034.22 seconds total)