Starting phenix.real_space_refine on Wed Sep 17 15:10:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rz8_19606/09_2025/8rz8_19606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rz8_19606/09_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_19606/09_2025/8rz8_19606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rz8_19606/09_2025/8rz8_19606.map" model { file = "/net/cci-nas-00/data/ceres_data/8rz8_19606/09_2025/8rz8_19606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rz8_19606/09_2025/8rz8_19606.cif" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.30, per 1000 atoms: 0.36 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: 0.95 Conformation dependent library (CDL) restraints added in 532.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.33 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: 1.55 Time building geometry restraints manager: 1.20 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: 3.100 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 11.370 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.090 ------------------------------------------------------------------------------- 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= 0.461 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.24), 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 ARG 0.016 0.001 ARG A 382 TYR 0.016 0.003 TYR B1011 PHE 0.012 0.003 PHE A 474 TRP 0.015 0.004 TRP B 579 HIS 0.008 0.002 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00696 ( 9401) covalent geometry : angle 1.18639 (12694) hydrogen bonds : bond 0.16572 ( 500) hydrogen bonds : angle 6.40772 ( 1463) *********************** 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 : 0.377 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: 0.1407 time to fit residues: 48.6026 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 : 0.357 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 613 ASN ** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.153121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.127200 restraints weight = 22481.347| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 3.17 r_work: 0.3639 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3650 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 956 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3650 r_free = 0.3650 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3650 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9401 Z= 0.179 Angle : 0.660 10.010 12694 Z= 0.343 Chirality : 0.043 0.187 1479 Planarity : 0.005 0.059 1600 Dihedral : 6.952 59.927 1294 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 2.94 % Allowed : 20.37 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.25), residues: 1129 helix: 0.61 (0.20), residues: 629 sheet: -1.29 (0.55), residues: 93 loop : -1.50 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 389 TYR 0.014 0.001 TYR A 299 PHE 0.027 0.002 PHE A 474 TRP 0.013 0.001 TRP A 764 HIS 0.007 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 9401) covalent geometry : angle 0.66043 (12694) hydrogen bonds : bond 0.05093 ( 500) hydrogen bonds : angle 5.00779 ( 1463) *********************** 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 282 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 480 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8127 (tp30) REVERT: A 617 VAL cc_start: 0.8237 (t) cc_final: 0.7959 (p) REVERT: A 635 LYS cc_start: 0.8265 (mptt) cc_final: 0.7962 (mptt) REVERT: A 722 VAL cc_start: 0.7436 (t) cc_final: 0.7137 (m) REVERT: A 743 SER cc_start: 0.8335 (t) cc_final: 0.7982 (m) REVERT: A 853 GLU cc_start: 0.7194 (pm20) cc_final: 0.6756 (pm20) REVERT: B 549 GLN cc_start: 0.7774 (pt0) cc_final: 0.7323 (pt0) REVERT: B 554 MET cc_start: 0.7412 (mmm) cc_final: 0.6706 (mmm) REVERT: B 591 ASN cc_start: 0.7592 (m-40) cc_final: 0.7337 (m110) REVERT: B 718 GLU cc_start: 0.7869 (pp20) cc_final: 0.7612 (pp20) REVERT: B 902 LYS cc_start: 0.8106 (mtmm) cc_final: 0.7816 (mtmm) outliers start: 30 outliers final: 17 residues processed: 264 average time/residue: 0.1367 time to fit residues: 46.4631 Evaluate side-chains 262 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 245 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 581 ILE Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 842 GLU 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 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 89 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 105 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 113 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 95 optimal weight: 0.7980 chunk 31 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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 B 917 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.153490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.129163 restraints weight = 15627.011| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.45 r_work: 0.3679 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- 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: 0.7158 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9401 Z= 0.192 Angle : 0.618 9.933 12694 Z= 0.321 Chirality : 0.043 0.203 1479 Planarity : 0.004 0.058 1600 Dihedral : 6.418 57.698 1279 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 2.94 % Allowed : 22.04 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.24), residues: 1129 helix: 0.66 (0.20), residues: 630 sheet: -1.27 (0.54), residues: 93 loop : -1.37 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 389 TYR 0.020 0.002 TYR A 408 PHE 0.030 0.002 PHE A 474 TRP 0.009 0.001 TRP A 764 HIS 0.008 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 9401) covalent geometry : angle 0.61814 (12694) hydrogen bonds : bond 0.04659 ( 500) hydrogen bonds : angle 4.83632 ( 1463) *********************** 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 271 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 241 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 357 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7020 (mm-30) REVERT: A 422 GLU cc_start: 0.7850 (tp30) cc_final: 0.6965 (tp30) REVERT: A 617 VAL cc_start: 0.8190 (t) cc_final: 0.7917 (p) REVERT: A 635 LYS cc_start: 0.8167 (mptt) cc_final: 0.7860 (mptt) REVERT: A 722 VAL cc_start: 0.7500 (t) cc_final: 0.7217 (m) REVERT: A 743 SER cc_start: 0.8227 (t) cc_final: 0.7894 (m) REVERT: A 814 LEU cc_start: 0.8004 (mt) cc_final: 0.7750 (mm) REVERT: B 549 GLN cc_start: 0.7725 (pt0) cc_final: 0.7123 (pt0) REVERT: B 554 MET cc_start: 0.7290 (mmm) cc_final: 0.6892 (mmm) REVERT: B 586 LYS cc_start: 0.7442 (mtmm) cc_final: 0.7202 (mtmm) REVERT: B 591 ASN cc_start: 0.7542 (m-40) cc_final: 0.7308 (m-40) REVERT: B 734 ARG cc_start: 0.7087 (ttp80) cc_final: 0.6661 (ttp80) REVERT: B 861 ASN cc_start: 0.8040 (m-40) cc_final: 0.7803 (m-40) REVERT: B 902 LYS cc_start: 0.8231 (mtmm) cc_final: 0.7829 (mtmm) REVERT: B 953 MET cc_start: 0.8002 (tpp) cc_final: 0.7487 (tpt) outliers start: 30 outliers final: 21 residues processed: 257 average time/residue: 0.1297 time to fit residues: 42.9146 Evaluate side-chains 255 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 234 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 386 ASP Chi-restraints excluded: chain A residue 577 ILE Chi-restraints excluded: chain A residue 626 GLU Chi-restraints excluded: chain A residue 656 TYR 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 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 852 GLN Chi-restraints excluded: chain B residue 871 LEU 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 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 96 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- 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** 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 = 0.4115 r_free = 0.4115 target = 0.153261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.127007 restraints weight = 22368.464| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 3.13 r_work: 0.3636 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 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 = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.2115 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= 0.212 Angle : 0.640 12.912 12694 Z= 0.326 Chirality : 0.044 0.238 1479 Planarity : 0.005 0.056 1600 Dihedral : 6.375 57.628 1278 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.53 % Allowed : 22.53 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.25), residues: 1129 helix: 0.61 (0.20), residues: 630 sheet: -1.27 (0.55), residues: 93 loop : -1.37 (0.30), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 389 TYR 0.022 0.002 TYR A 299 PHE 0.026 0.002 PHE A 474 TRP 0.012 0.002 TRP A 764 HIS 0.008 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 9401) covalent geometry : angle 0.63996 (12694) hydrogen bonds : bond 0.04476 ( 500) hydrogen bonds : angle 4.82739 ( 1463) *********************** 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 272 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 236 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 LEU cc_start: 0.7860 (mm) cc_final: 0.7629 (mp) REVERT: A 384 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.7110 (m-80) REVERT: A 617 VAL cc_start: 0.8221 (t) cc_final: 0.7957 (p) REVERT: A 635 LYS cc_start: 0.8301 (mptt) cc_final: 0.7963 (mptt) REVERT: A 722 VAL cc_start: 0.7538 (t) cc_final: 0.7287 (m) REVERT: A 743 SER cc_start: 0.8292 (t) cc_final: 0.7965 (m) REVERT: A 814 LEU cc_start: 0.8099 (mt) cc_final: 0.7842 (mm) REVERT: B 549 GLN cc_start: 0.7790 (pt0) cc_final: 0.7101 (pt0) REVERT: B 554 MET cc_start: 0.7372 (mmm) cc_final: 0.7055 (mmm) REVERT: B 591 ASN cc_start: 0.7658 (m-40) cc_final: 0.7438 (m-40) REVERT: B 861 ASN cc_start: 0.8145 (m-40) cc_final: 0.7907 (m-40) REVERT: B 902 LYS cc_start: 0.8194 (mtmm) cc_final: 0.7800 (mtmm) REVERT: B 953 MET cc_start: 0.8031 (tpp) cc_final: 0.7556 (tpt) REVERT: B 972 VAL cc_start: 0.7794 (t) cc_final: 0.7458 (m) REVERT: B 1058 GLN cc_start: 0.8482 (tt0) cc_final: 0.8280 (tt0) outliers start: 36 outliers final: 29 residues processed: 257 average time/residue: 0.1363 time to fit residues: 45.2135 Evaluate side-chains 262 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 577 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 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 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 1003 SER Chi-restraints excluded: chain B residue 1005 THR 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 18 optimal weight: 0.3980 chunk 4 optimal weight: 4.9990 chunk 102 optimal weight: 0.4980 chunk 99 optimal weight: 0.5980 chunk 1 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 43 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 A 690 GLN B 544 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.154788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.131477 restraints weight = 12983.641| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 2.14 r_work: 0.3736 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3585 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3585 r_free = 0.3585 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3585 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9401 Z= 0.163 Angle : 0.598 11.041 12694 Z= 0.307 Chirality : 0.043 0.216 1479 Planarity : 0.004 0.052 1600 Dihedral : 6.313 55.816 1278 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.82 % Allowed : 22.43 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.25), residues: 1129 helix: 0.65 (0.20), residues: 637 sheet: -1.19 (0.55), residues: 93 loop : -1.26 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 389 TYR 0.025 0.001 TYR A 299 PHE 0.023 0.002 PHE A 474 TRP 0.008 0.001 TRP A 764 HIS 0.009 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 9401) covalent geometry : angle 0.59784 (12694) hydrogen bonds : bond 0.04168 ( 500) hydrogen bonds : angle 4.73425 ( 1463) *********************** 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 283 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 244 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.7545 (OUTLIER) cc_final: 0.7070 (m-80) REVERT: A 450 PHE cc_start: 0.7503 (t80) cc_final: 0.7229 (t80) REVERT: A 617 VAL cc_start: 0.8230 (t) cc_final: 0.7971 (p) REVERT: A 631 ARG cc_start: 0.7555 (mtp180) cc_final: 0.7344 (ttp-110) REVERT: A 635 LYS cc_start: 0.8313 (mptt) cc_final: 0.7969 (mptt) REVERT: A 690 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.7833 (mt0) REVERT: A 722 VAL cc_start: 0.7544 (t) cc_final: 0.7283 (m) REVERT: A 743 SER cc_start: 0.8374 (t) cc_final: 0.8038 (m) REVERT: A 814 LEU cc_start: 0.8123 (mt) cc_final: 0.7858 (mm) REVERT: B 549 GLN cc_start: 0.7858 (pt0) cc_final: 0.7599 (pt0) REVERT: B 591 ASN cc_start: 0.7755 (m-40) cc_final: 0.7522 (m110) REVERT: B 653 GLN cc_start: 0.8488 (mm110) cc_final: 0.8084 (mm110) REVERT: B 690 ASN cc_start: 0.7942 (t0) cc_final: 0.7395 (t0) REVERT: B 793 ASN cc_start: 0.8275 (m-40) cc_final: 0.8057 (m110) REVERT: B 953 MET cc_start: 0.8059 (tpp) cc_final: 0.7652 (tpt) REVERT: B 972 VAL cc_start: 0.7913 (t) cc_final: 0.7574 (m) REVERT: B 1058 GLN cc_start: 0.8585 (tt0) cc_final: 0.8373 (tt0) outliers start: 39 outliers final: 30 residues processed: 265 average time/residue: 0.1354 time to fit residues: 46.5637 Evaluate side-chains 266 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 234 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 577 ILE 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 584 LEU 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 860 LYS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 47 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.0570 chunk 41 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 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 = 0.4132 r_free = 0.4132 target = 0.154698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.128507 restraints weight = 22548.682| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 3.15 r_work: 0.3656 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3653 r_free = 0.3653 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9401 Z= 0.173 Angle : 0.606 10.745 12694 Z= 0.310 Chirality : 0.043 0.230 1479 Planarity : 0.004 0.051 1600 Dihedral : 6.308 55.840 1278 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.82 % Allowed : 23.02 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.25), residues: 1129 helix: 0.70 (0.20), residues: 638 sheet: -0.75 (0.58), residues: 86 loop : -1.23 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 389 TYR 0.024 0.001 TYR A 299 PHE 0.020 0.001 PHE A 474 TRP 0.010 0.001 TRP A 764 HIS 0.008 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00390 ( 9401) covalent geometry : angle 0.60579 (12694) hydrogen bonds : bond 0.04131 ( 500) hydrogen bonds : angle 4.71423 ( 1463) *********************** 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 273 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 234 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.7478 (OUTLIER) cc_final: 0.7022 (m-80) REVERT: A 450 PHE cc_start: 0.7384 (t80) cc_final: 0.7113 (t80) REVERT: A 617 VAL cc_start: 0.8189 (t) cc_final: 0.7927 (p) REVERT: A 635 LYS cc_start: 0.8274 (mptt) cc_final: 0.7928 (mptt) REVERT: A 722 VAL cc_start: 0.7495 (t) cc_final: 0.7257 (m) REVERT: A 743 SER cc_start: 0.8297 (t) cc_final: 0.7925 (m) REVERT: A 814 LEU cc_start: 0.8085 (mt) cc_final: 0.7813 (mm) REVERT: B 591 ASN cc_start: 0.7630 (m-40) cc_final: 0.7412 (m-40) REVERT: B 653 GLN cc_start: 0.8506 (mm110) cc_final: 0.8101 (mm110) REVERT: B 861 ASN cc_start: 0.8000 (m110) cc_final: 0.7790 (m-40) REVERT: B 944 ASN cc_start: 0.7926 (t0) cc_final: 0.7636 (t0) REVERT: B 953 MET cc_start: 0.8012 (tpp) cc_final: 0.7599 (tpt) REVERT: B 972 VAL cc_start: 0.7811 (t) cc_final: 0.7461 (m) REVERT: B 1058 GLN cc_start: 0.8512 (tt0) cc_final: 0.8276 (tt0) outliers start: 39 outliers final: 30 residues processed: 258 average time/residue: 0.1377 time to fit residues: 45.8853 Evaluate side-chains 265 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 577 ILE Chi-restraints excluded: chain A residue 656 TYR 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 656 ILE 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 860 LYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 2 optimal weight: 0.9990 chunk 60 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 70 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.154037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.130692 restraints weight = 12974.594| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.14 r_work: 0.3723 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9401 Z= 0.193 Angle : 0.612 8.282 12694 Z= 0.315 Chirality : 0.044 0.232 1479 Planarity : 0.005 0.051 1600 Dihedral : 6.342 56.445 1278 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.31 % Allowed : 22.72 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.25), residues: 1129 helix: 0.70 (0.20), residues: 636 sheet: -0.78 (0.58), residues: 86 loop : -1.23 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 631 TYR 0.023 0.002 TYR A 299 PHE 0.019 0.002 PHE A 474 TRP 0.011 0.001 TRP A 764 HIS 0.008 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00436 ( 9401) covalent geometry : angle 0.61233 (12694) hydrogen bonds : bond 0.04122 ( 500) hydrogen bonds : angle 4.72046 ( 1463) *********************** 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 282 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 238 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7076 (m-80) REVERT: A 414 LEU cc_start: 0.6983 (OUTLIER) cc_final: 0.6674 (mt) REVERT: A 422 GLU cc_start: 0.8071 (tp30) cc_final: 0.6925 (tp30) REVERT: A 431 LEU cc_start: 0.8480 (tp) cc_final: 0.8274 (tt) REVERT: A 617 VAL cc_start: 0.8244 (t) cc_final: 0.7980 (p) REVERT: A 690 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7770 (mt0) REVERT: A 722 VAL cc_start: 0.7545 (t) cc_final: 0.7314 (m) REVERT: A 743 SER cc_start: 0.8355 (t) cc_final: 0.8018 (m) REVERT: A 814 LEU cc_start: 0.8167 (mt) cc_final: 0.7900 (mm) REVERT: B 591 ASN cc_start: 0.7760 (m-40) cc_final: 0.7538 (m-40) REVERT: B 653 GLN cc_start: 0.8611 (mm110) cc_final: 0.8179 (mm110) REVERT: B 861 ASN cc_start: 0.8097 (m110) cc_final: 0.7865 (m-40) REVERT: B 944 ASN cc_start: 0.7980 (t0) cc_final: 0.7680 (t0) REVERT: B 972 VAL cc_start: 0.7904 (t) cc_final: 0.7560 (m) REVERT: B 1058 GLN cc_start: 0.8592 (tt0) cc_final: 0.8341 (tt0) outliers start: 44 outliers final: 34 residues processed: 263 average time/residue: 0.1380 time to fit residues: 46.9333 Evaluate side-chains 267 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 230 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 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 463 VAL Chi-restraints excluded: chain A residue 626 GLU 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 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 656 ILE 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 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 860 LYS Chi-restraints excluded: chain B residue 871 LEU Chi-restraints excluded: chain B residue 882 THR Chi-restraints excluded: chain B residue 889 GLU 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 Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 86 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 70 optimal weight: 0.4980 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 0.0870 chunk 81 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 97 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- 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 671 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 GLN ** A 783 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 544 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1071 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.155215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.131133 restraints weight = 15064.840| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.38 r_work: 0.3723 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- 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: 0.7285 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9401 Z= 0.158 Angle : 0.613 10.016 12694 Z= 0.312 Chirality : 0.043 0.238 1479 Planarity : 0.005 0.049 1600 Dihedral : 6.091 55.731 1276 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.92 % Allowed : 24.00 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.25), residues: 1129 helix: 0.79 (0.20), residues: 642 sheet: -0.73 (0.58), residues: 86 loop : -1.23 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 631 TYR 0.024 0.001 TYR A 408 PHE 0.017 0.001 PHE A 474 TRP 0.009 0.001 TRP A 764 HIS 0.009 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9401) covalent geometry : angle 0.61294 (12694) hydrogen bonds : bond 0.03962 ( 500) hydrogen bonds : angle 4.67226 ( 1463) *********************** 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 271 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.7575 (OUTLIER) cc_final: 0.7068 (m-80) REVERT: A 414 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6641 (mt) REVERT: A 422 GLU cc_start: 0.8058 (tp30) cc_final: 0.6934 (tp30) REVERT: A 431 LEU cc_start: 0.8507 (tp) cc_final: 0.8300 (tt) REVERT: A 575 ASP cc_start: 0.8197 (t0) cc_final: 0.7997 (t0) REVERT: A 617 VAL cc_start: 0.8240 (t) cc_final: 0.7980 (p) REVERT: A 690 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7381 (mp10) REVERT: A 722 VAL cc_start: 0.7553 (t) cc_final: 0.7325 (m) REVERT: A 743 SER cc_start: 0.8393 (t) cc_final: 0.8031 (m) REVERT: A 814 LEU cc_start: 0.8165 (mt) cc_final: 0.7903 (mm) REVERT: B 591 ASN cc_start: 0.7799 (m-40) cc_final: 0.7589 (m-40) REVERT: B 649 LYS cc_start: 0.8320 (ttpp) cc_final: 0.8015 (tttm) REVERT: B 653 GLN cc_start: 0.8631 (mm110) cc_final: 0.8188 (mm110) REVERT: B 861 ASN cc_start: 0.8130 (m110) cc_final: 0.7907 (m-40) REVERT: B 944 ASN cc_start: 0.7995 (t0) cc_final: 0.7698 (t0) REVERT: B 972 VAL cc_start: 0.7956 (t) cc_final: 0.7614 (m) REVERT: B 1058 GLN cc_start: 0.8606 (tt0) cc_final: 0.8359 (tt0) REVERT: B 1099 THR cc_start: 0.7584 (m) cc_final: 0.7379 (p) outliers start: 40 outliers final: 31 residues processed: 253 average time/residue: 0.1280 time to fit residues: 41.8081 Evaluate side-chains 268 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU 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 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 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 656 ILE 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 850 THR Chi-restraints excluded: chain B residue 852 GLN Chi-restraints excluded: chain B residue 860 LYS 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 Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.0040 chunk 59 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 104 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.6992 ------------------------------------------------------------------------------- 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 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.154363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.129629 restraints weight = 17315.900| |-----------------------------------------------------------------------------| r_work (start): 0.3794 rms_B_bonded: 2.62 r_work: 0.3675 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3691 r_free = 0.3691 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 = 0.3691 r_free = 0.3691 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9401 Z= 0.185 Angle : 0.612 7.960 12694 Z= 0.314 Chirality : 0.044 0.232 1479 Planarity : 0.005 0.050 1600 Dihedral : 6.117 57.597 1276 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 3.72 % Allowed : 23.60 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.25), residues: 1129 helix: 0.77 (0.20), residues: 642 sheet: -0.75 (0.58), residues: 86 loop : -1.22 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 631 TYR 0.022 0.001 TYR A 299 PHE 0.016 0.001 PHE A 474 TRP 0.010 0.001 TRP A 764 HIS 0.008 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00419 ( 9401) covalent geometry : angle 0.61224 (12694) hydrogen bonds : bond 0.04003 ( 500) hydrogen bonds : angle 4.67209 ( 1463) *********************** 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 274 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 236 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: A 414 LEU cc_start: 0.6844 (OUTLIER) cc_final: 0.6557 (mt) REVERT: A 422 GLU cc_start: 0.8019 (tp30) cc_final: 0.6856 (tp30) REVERT: A 431 LEU cc_start: 0.8384 (tp) cc_final: 0.8171 (tt) REVERT: A 617 VAL cc_start: 0.8169 (t) cc_final: 0.7910 (p) REVERT: A 690 GLN cc_start: 0.7975 (OUTLIER) cc_final: 0.7305 (mp10) REVERT: A 722 VAL cc_start: 0.7515 (t) cc_final: 0.7293 (m) REVERT: A 743 SER cc_start: 0.8211 (t) cc_final: 0.7870 (m) REVERT: A 814 LEU cc_start: 0.8070 (mt) cc_final: 0.7808 (mm) REVERT: B 591 ASN cc_start: 0.7572 (m-40) cc_final: 0.7360 (m-40) REVERT: B 649 LYS cc_start: 0.8266 (ttpp) cc_final: 0.7939 (tttm) REVERT: B 653 GLN cc_start: 0.8563 (mm110) cc_final: 0.8168 (mm110) REVERT: B 861 ASN cc_start: 0.7955 (m110) cc_final: 0.7742 (m-40) REVERT: B 944 ASN cc_start: 0.7940 (t0) cc_final: 0.7624 (t0) REVERT: B 972 VAL cc_start: 0.7758 (t) cc_final: 0.7391 (m) REVERT: B 1058 GLN cc_start: 0.8437 (tt0) cc_final: 0.8195 (tt0) outliers start: 38 outliers final: 30 residues processed: 260 average time/residue: 0.1347 time to fit residues: 45.2160 Evaluate side-chains 269 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 LEU 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 463 VAL 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 585 LEU Chi-restraints excluded: chain B residue 607 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 656 ILE 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 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 Chi-restraints excluded: chain B residue 1056 LEU Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 105 optimal weight: 0.0670 chunk 89 optimal weight: 0.6980 chunk 6 optimal weight: 0.0000 chunk 88 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 1 optimal weight: 0.0980 overall best weight: 0.2922 ------------------------------------------------------------------------------- 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 A 799 ASN B 544 ASN ** B 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.156815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.132522 restraints weight = 15514.803| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 2.46 r_work: 0.3739 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 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 = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9401 Z= 0.132 Angle : 0.607 10.007 12694 Z= 0.309 Chirality : 0.043 0.338 1479 Planarity : 0.005 0.047 1600 Dihedral : 6.038 56.042 1276 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.33 % Allowed : 24.19 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.25), residues: 1129 helix: 0.90 (0.20), residues: 642 sheet: -1.58 (0.51), residues: 102 loop : -1.16 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 715 TYR 0.016 0.001 TYR A 299 PHE 0.012 0.001 PHE A 474 TRP 0.009 0.001 TRP B 807 HIS 0.009 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9401) covalent geometry : angle 0.60714 (12694) hydrogen bonds : bond 0.03779 ( 500) hydrogen bonds : angle 4.62353 ( 1463) ********************** 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 273 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 239 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 384 PHE cc_start: 0.7370 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: A 414 LEU cc_start: 0.6707 (OUTLIER) cc_final: 0.6451 (mt) REVERT: A 422 GLU cc_start: 0.7951 (tp30) cc_final: 0.7043 (tp30) REVERT: A 431 LEU cc_start: 0.8403 (tp) cc_final: 0.8180 (tt) REVERT: A 617 VAL cc_start: 0.8124 (t) cc_final: 0.7871 (p) REVERT: A 690 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7300 (mp10) REVERT: A 743 SER cc_start: 0.8181 (t) cc_final: 0.7826 (m) REVERT: A 814 LEU cc_start: 0.8007 (mt) cc_final: 0.7748 (mm) REVERT: B 591 ASN cc_start: 0.7498 (m-40) cc_final: 0.7224 (m110) REVERT: B 649 LYS cc_start: 0.8202 (ttpp) cc_final: 0.7844 (tttm) REVERT: B 653 GLN cc_start: 0.8488 (mm110) cc_final: 0.8090 (mm110) REVERT: B 798 GLN cc_start: 0.6295 (tm-30) cc_final: 0.5708 (tm-30) REVERT: B 944 ASN cc_start: 0.7864 (t0) cc_final: 0.7552 (t0) REVERT: B 972 VAL cc_start: 0.7723 (t) cc_final: 0.7361 (m) REVERT: B 1058 GLN cc_start: 0.8370 (tt0) cc_final: 0.8116 (tt0) outliers start: 34 outliers final: 25 residues processed: 260 average time/residue: 0.1390 time to fit residues: 46.5776 Evaluate side-chains 264 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 236 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 280 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 607 VAL Chi-restraints excluded: chain B residue 618 LEU Chi-restraints excluded: chain B residue 632 LYS Chi-restraints excluded: chain B residue 656 ILE 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 850 THR Chi-restraints excluded: chain B residue 852 GLN 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 Chi-restraints excluded: chain B residue 1060 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 10 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 58 optimal weight: 0.0040 chunk 25 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 52 optimal weight: 0.9990 chunk 37 optimal weight: 0.0470 chunk 68 optimal weight: 0.0770 overall best weight: 0.1848 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 ASN ** A 662 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 690 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 = 0.4169 r_free = 0.4169 target = 0.157998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.133068 restraints weight = 17684.725| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.69 r_work: 0.3720 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3720 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3736 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3736 r_free = 0.3736 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 = 0.3736 r_free = 0.3736 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 953 | |-----------------------------------------------------------------------------| r_final: 0.3736 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9401 Z= 0.122 Angle : 0.604 10.069 12694 Z= 0.304 Chirality : 0.043 0.320 1479 Planarity : 0.004 0.048 1600 Dihedral : 5.854 56.421 1274 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.94 % Allowed : 24.39 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.05 (0.25), residues: 1129 helix: 0.98 (0.20), residues: 642 sheet: -1.13 (0.54), residues: 92 loop : -1.19 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 631 TYR 0.016 0.001 TYR A 405 PHE 0.012 0.001 PHE A 474 TRP 0.009 0.001 TRP B 807 HIS 0.008 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 9401) covalent geometry : angle 0.60381 (12694) hydrogen bonds : bond 0.03627 ( 500) hydrogen bonds : angle 4.57450 ( 1463) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4131.96 seconds wall clock time: 71 minutes 3.73 seconds (4263.73 seconds total)