Starting phenix.real_space_refine on Fri Jul 3 05:58:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kx9_23063/07_2026/7kx9_23063.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kx9_23063/07_2026/7kx9_23063.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7kx9_23063/07_2026/7kx9_23063.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kx9_23063/07_2026/7kx9_23063.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kx9_23063/07_2026/7kx9_23063.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kx9_23063/07_2026/7kx9_23063.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7kx9_23063/07_2026/7kx9_23063.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kx9_23063/07_2026/7kx9_23063.cif" } resolution = 3.5 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= 0.003 sd= 0.033 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 25 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 40 5.49 5 Mg 2 5.21 5 S 33 5.16 5 C 4015 2.51 5 N 1170 2.21 5 O 1318 1.98 5 H 5846 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12424 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 11133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 11133 Classifications: {'peptide': 734} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 38, 'TRANS': 695} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 201 Unresolved non-hydrogen angles: 254 Unresolved non-hydrogen dihedrals: 161 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 4, 'ASP:plan': 5, 'ARG:plan': 5, 'GLN:plan1': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 774 Classifications: {'RNA': 24} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 8, 'rna3p_pyr': 8} Link IDs: {'rna2p': 7, 'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "C" Number of atoms: 515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 515 Classifications: {'RNA': 16} Modifications used: {'3*END': 1, 'rna3p_pur': 9, 'rna3p_pyr': 7} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.37, per 1000 atoms: 0.19 Number of scatterers: 12424 At special positions: 0 Unit cell: (79.35, 109.25, 75.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 33 16.00 P 40 15.00 Mg 2 11.99 O 1318 8.00 N 1170 7.00 C 4015 6.00 H 5846 1.00 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.23 Conformation dependent library (CDL) restraints added in 429.0 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1398 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 11 sheets defined 33.9% alpha, 16.2% beta 10 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 267 through 277 removed outlier: 3.644A pdb=" N GLU A 277 " --> pdb=" O GLN A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 347 removed outlier: 3.708A pdb=" N ARG A 345 " --> pdb=" O LYS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 412 Processing helix chain 'A' and resid 458 through 460 No H-bonds generated for 'chain 'A' and resid 458 through 460' Processing helix chain 'A' and resid 465 through 474 Processing helix chain 'A' and resid 521 through 527 Processing helix chain 'A' and resid 528 through 539 removed outlier: 3.641A pdb=" N VAL A 536 " --> pdb=" O LYS A 532 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N HIS A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 558 Processing helix chain 'A' and resid 559 through 570 removed outlier: 3.551A pdb=" N SER A 563 " --> pdb=" O THR A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 631 through 646 Processing helix chain 'A' and resid 647 through 650 Processing helix chain 'A' and resid 665 through 677 Processing helix chain 'A' and resid 692 through 705 Processing helix chain 'A' and resid 717 through 721 removed outlier: 4.297A pdb=" N GLN A 721 " --> pdb=" O THR A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 739 removed outlier: 3.560A pdb=" N LEU A 734 " --> pdb=" O GLN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 797 through 819 Processing helix chain 'A' and resid 836 through 851 removed outlier: 4.021A pdb=" N VAL A 840 " --> pdb=" O ARG A 836 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 841 " --> pdb=" O GLU A 837 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N VAL A 845 " --> pdb=" O SER A 841 " (cutoff:3.500A) Proline residue: A 846 - end of helix removed outlier: 3.883A pdb=" N CYS A 851 " --> pdb=" O GLN A 847 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 856 removed outlier: 3.616A pdb=" N PHE A 855 " --> pdb=" O PHE A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 930 through 941 Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 955 through 969 removed outlier: 3.651A pdb=" N ASN A 959 " --> pdb=" O PRO A 955 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 578 through 579 removed outlier: 3.804A pdb=" N LEU A 578 " --> pdb=" O ALA A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 247 removed outlier: 4.439A pdb=" N LEU A 387 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 390 " --> pdb=" O ALA A 379 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 379 " --> pdb=" O VAL A 390 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP A 392 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP A 373 " --> pdb=" O ARG A 396 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N TYR A 376 " --> pdb=" O TYR A 356 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR A 357 " --> pdb=" O GLN A 350 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 287 through 288 removed outlier: 3.504A pdb=" N VAL A 287 " --> pdb=" O TYR A 294 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER A 322 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 309 Processing sheet with id=AA6, first strand: chain 'A' and resid 438 through 441 removed outlier: 3.512A pdb=" N ARG A 438 " --> pdb=" O THR A 433 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 444 through 445 Processing sheet with id=AA8, first strand: chain 'A' and resid 454 through 456 Processing sheet with id=AA9, first strand: chain 'A' and resid 596 through 598 removed outlier: 3.678A pdb=" N ALA A 746 " --> pdb=" O LEU A 591 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 660 through 661 removed outlier: 7.529A pdb=" N VAL A 661 " --> pdb=" O VAL A 625 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE A 627 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ALA A 624 " --> pdb=" O VAL A 685 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N VAL A 687 " --> pdb=" O ALA A 624 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N LEU A 626 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 684 " --> pdb=" O GLN A 712 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU A 714 " --> pdb=" O VAL A 684 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE A 686 " --> pdb=" O LEU A 714 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.957A pdb=" N MET A 755 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 8.273A pdb=" N PHE A 828 " --> pdb=" O MET A 755 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N VAL A 757 " --> pdb=" O PHE A 828 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU A 863 " --> pdb=" O ASP A 925 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N ASP A 925 " --> pdb=" O LEU A 863 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N VAL A 865 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 923 " --> pdb=" O VAL A 865 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 600 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 2.86 Time building geometry restraints manager: 1.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 5834 1.03 - 1.23: 40 1.23 - 1.42: 2910 1.42 - 1.61: 3808 1.61 - 1.81: 54 Bond restraints: 12646 Sorted by residual: bond pdb=" C2 OMG B 24 " pdb=" N3 OMG B 24 " ideal model delta sigma weight residual 1.308 1.478 -0.170 2.00e-02 2.50e+03 7.27e+01 bond pdb=" N3 OMG B 24 " pdb=" C4 OMG B 24 " ideal model delta sigma weight residual 1.341 1.493 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" C2 OMG B 24 " pdb=" N2 OMG B 24 " ideal model delta sigma weight residual 1.344 1.487 -0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" C5 OMG B 24 " pdb=" C6 OMG B 24 " ideal model delta sigma weight residual 1.424 1.544 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" N1 OMG B 24 " pdb=" C2 OMG B 24 " ideal model delta sigma weight residual 1.365 1.439 -0.074 2.00e-02 2.50e+03 1.36e+01 ... (remaining 12641 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.48: 22689 5.48 - 10.96: 13 10.96 - 16.44: 0 16.44 - 21.92: 0 21.92 - 27.40: 4 Bond angle restraints: 22706 Sorted by residual: angle pdb=" O3' U B 10 " pdb=" P U B 11 " pdb=" OP1 U B 11 " ideal model delta sigma weight residual 108.00 80.60 27.40 3.00e+00 1.11e-01 8.34e+01 angle pdb=" C1' OMG B 24 " pdb=" N9 OMG B 24 " pdb=" C8 OMG B 24 " ideal model delta sigma weight residual 127.59 100.49 27.10 3.00e+00 1.11e-01 8.16e+01 angle pdb=" C1' OMG B 24 " pdb=" N9 OMG B 24 " pdb=" C4 OMG B 24 " ideal model delta sigma weight residual 125.50 151.60 -26.10 3.00e+00 1.11e-01 7.57e+01 angle pdb=" O3' U B 10 " pdb=" P U B 11 " pdb=" OP2 U B 11 " ideal model delta sigma weight residual 108.00 83.25 24.75 3.00e+00 1.11e-01 6.80e+01 angle pdb=" OP1 U B 11 " pdb=" P U B 11 " pdb=" OP2 U B 11 " ideal model delta sigma weight residual 119.60 130.39 -10.79 3.00e+00 1.11e-01 1.29e+01 ... (remaining 22701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.09: 5508 24.09 - 48.19: 301 48.19 - 72.28: 39 72.28 - 96.37: 12 96.37 - 120.47: 4 Dihedral angle restraints: 5864 sinusoidal: 3359 harmonic: 2505 Sorted by residual: dihedral pdb=" CA ARG A 286 " pdb=" C ARG A 286 " pdb=" N VAL A 287 " pdb=" CA VAL A 287 " ideal model delta harmonic sigma weight residual 180.00 159.66 20.34 0 5.00e+00 4.00e-02 1.65e+01 dihedral pdb=" CA SER A 850 " pdb=" C SER A 850 " pdb=" N CYS A 851 " pdb=" CA CYS A 851 " ideal model delta harmonic sigma weight residual -180.00 -159.83 -20.17 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA HIS A 895 " pdb=" C HIS A 895 " pdb=" N THR A 896 " pdb=" CA THR A 896 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 5861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.384: 1088 0.384 - 0.768: 0 0.768 - 1.152: 0 1.152 - 1.536: 0 1.536 - 1.921: 1 Chirality restraints: 1089 Sorted by residual: chirality pdb=" P U B 11 " pdb=" OP1 U B 11 " pdb=" OP2 U B 11 " pdb=" O5' U B 11 " both_signs ideal model delta sigma weight residual True 2.41 0.49 1.92 2.00e-01 2.50e+01 9.22e+01 chirality pdb=" C1' G C 22 " pdb=" O4' G C 22 " pdb=" C2' G C 22 " pdb=" N9 G C 22 " both_signs ideal model delta sigma weight residual False 2.46 2.26 0.20 2.00e-01 2.50e+01 9.65e-01 chirality pdb=" CA MET A 398 " pdb=" N MET A 398 " pdb=" C MET A 398 " pdb=" CB MET A 398 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.36e-01 ... (remaining 1086 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 860 " 0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO A 861 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 861 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 861 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 397 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.54e+00 pdb=" C VAL A 397 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 397 " -0.010 2.00e-02 2.50e+03 pdb=" N MET A 398 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C 22 " 0.019 2.00e-02 2.50e+03 8.46e-03 2.50e+00 pdb=" N9 G C 22 " -0.024 2.00e-02 2.50e+03 pdb=" C8 G C 22 " -0.003 2.00e-02 2.50e+03 pdb=" N7 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C 22 " 0.002 2.00e-02 2.50e+03 pdb=" O6 G C 22 " 0.004 2.00e-02 2.50e+03 pdb=" N1 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" C2 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G C 22 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G C 22 " 0.000 2.00e-02 2.50e+03 pdb=" C4 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" H8 G C 22 " 0.001 2.00e-02 2.50e+03 pdb=" H1 G C 22 " 0.000 2.00e-02 2.50e+03 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.86: 52 1.86 - 2.54: 10717 2.54 - 3.23: 36642 3.23 - 3.91: 45816 3.91 - 4.60: 73739 Nonbonded interactions: 166966 Sorted by model distance: nonbonded pdb="HH21 ARG A 953 " pdb=" OP2 U B 6 " model vdw 1.172 2.450 nonbonded pdb=" HD1 HIS A 962 " pdb="MG MG A1002 " model vdw 1.466 1.700 nonbonded pdb=" HE2 TYR A 468 " pdb=" H3' OMG B 24 " model vdw 1.497 2.270 nonbonded pdb="HE22 GLN A 735 " pdb="MG MG A1001 " model vdw 1.547 1.700 nonbonded pdb=" O ASN A 663 " pdb=" HG SER A 668 " model vdw 1.548 2.450 ... (remaining 166961 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.090 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 14.790 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 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 : 0.012 0.790 6801 Z= 1.025 Angle : 0.934 27.403 9412 Z= 0.453 Chirality : 0.074 1.921 1089 Planarity : 0.005 0.044 1062 Dihedral : 14.994 120.468 2621 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.54 % Favored : 88.46 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.67 % 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 are not related in a simple way. whole: -3.70 (0.30), residues: 728 helix: -0.96 (0.34), residues: 224 sheet: -3.45 (0.34), residues: 187 loop : -2.83 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 629 TYR 0.011 0.002 TYR A 435 PHE 0.009 0.001 PHE A 340 TRP 0.006 0.001 TRP A 623 HIS 0.009 0.001 HIS A 487 Details of bonding type rmsd/Z covalent geometry : bond 0.00777 / 0.36 ( 6800) covalent geometry : angle 0.93373 / 0.45 ( 9412) hydrogen bonds : bond 0.23118 / 16.37 ( 241) hydrogen bonds : angle 8.95913 / 6.31 ( 650) Misc. bond : bond 0.79026 / 41.59 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 86 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8702 (mt) cc_final: 0.8457 (mt) REVERT: A 908 GLN cc_start: 0.7761 (tp40) cc_final: 0.7422 (tp40) outliers start: 1 outliers final: 1 residues processed: 85 average time/residue: 0.1830 time to fit residues: 20.6474 Evaluate side-chains 68 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 487 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 30.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 640 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.147018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.102487 restraints weight = 26282.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108626 restraints weight = 12604.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112380 restraints weight = 8305.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.114615 restraints weight = 6499.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115956 restraints weight = 5608.355| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6801 Z= 0.176 Angle : 0.760 27.375 9412 Z= 0.356 Chirality : 0.071 1.881 1089 Planarity : 0.005 0.089 1062 Dihedral : 12.943 116.372 1276 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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 are not related in a simple way. whole: -2.97 (0.30), residues: 728 helix: -0.07 (0.34), residues: 220 sheet: -2.97 (0.37), residues: 171 loop : -2.71 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 671 TYR 0.012 0.001 TYR A 376 PHE 0.015 0.001 PHE A 340 TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.18 ( 6800) covalent geometry : angle 0.75968 / 0.36 ( 9412) hydrogen bonds : bond 0.05734 / 4.17 ( 241) hydrogen bonds : angle 6.31968 / 4.53 ( 650) Misc. bond : bond 0.00301 / 0.16 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7327 (mmp) cc_final: 0.6818 (mmp) REVERT: A 621 LEU cc_start: 0.8716 (mt) cc_final: 0.8481 (mt) REVERT: A 793 GLN cc_start: 0.6630 (mp10) cc_final: 0.4475 (mp10) REVERT: A 812 LYS cc_start: 0.8701 (tppt) cc_final: 0.8476 (tppt) REVERT: A 908 GLN cc_start: 0.7564 (tp40) cc_final: 0.7274 (tp40) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1826 time to fit residues: 18.1564 Evaluate side-chains 71 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 27 optimal weight: 10.0000 chunk 9 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 24 optimal weight: 20.0000 chunk 48 optimal weight: 3.9990 chunk 31 optimal weight: 9.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.147293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.102616 restraints weight = 26830.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.108829 restraints weight = 12709.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112712 restraints weight = 8365.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.114981 restraints weight = 6548.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116432 restraints weight = 5648.071| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6801 Z= 0.136 Angle : 0.693 26.895 9412 Z= 0.320 Chirality : 0.071 1.917 1089 Planarity : 0.004 0.057 1062 Dihedral : 12.758 125.338 1274 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 0.17 % Allowed : 6.33 % Favored : 93.50 % 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 are not related in a simple way. whole: -2.51 (0.31), residues: 728 helix: 0.53 (0.36), residues: 220 sheet: -2.78 (0.37), residues: 173 loop : -2.55 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 671 TYR 0.010 0.001 TYR A 376 PHE 0.013 0.001 PHE A 340 TRP 0.008 0.001 TRP A 569 HIS 0.010 0.001 HIS A 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.14 ( 6800) covalent geometry : angle 0.69350 / 0.32 ( 9412) hydrogen bonds : bond 0.04661 / 3.42 ( 241) hydrogen bonds : angle 5.68504 / 4.08 ( 650) Misc. bond : bond 0.00166 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 75 time to evaluate : 0.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8742 (mt) cc_final: 0.8505 (mt) REVERT: A 801 HIS cc_start: 0.8357 (t70) cc_final: 0.8112 (t-170) REVERT: A 812 LYS cc_start: 0.8720 (tppt) cc_final: 0.8416 (tppt) outliers start: 1 outliers final: 1 residues processed: 75 average time/residue: 0.1640 time to fit residues: 16.2401 Evaluate side-chains 71 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 74 optimal weight: 30.0000 chunk 56 optimal weight: 8.9990 chunk 9 optimal weight: 40.0000 chunk 72 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 7 optimal weight: 40.0000 chunk 22 optimal weight: 30.0000 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.146041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101587 restraints weight = 26265.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107725 restraints weight = 12522.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.111516 restraints weight = 8236.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113741 restraints weight = 6451.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.115170 restraints weight = 5580.216| |-----------------------------------------------------------------------------| r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6801 Z= 0.159 Angle : 0.686 27.008 9412 Z= 0.316 Chirality : 0.071 1.911 1089 Planarity : 0.004 0.056 1062 Dihedral : 12.673 125.886 1274 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.67 % Allowed : 6.83 % Favored : 92.50 % 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 are not related in a simple way. whole: -2.28 (0.31), residues: 728 helix: 0.71 (0.36), residues: 222 sheet: -2.65 (0.38), residues: 169 loop : -2.44 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 879 TYR 0.011 0.001 TYR A 376 PHE 0.013 0.001 PHE A 340 TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 6800) covalent geometry : angle 0.68624 / 0.32 ( 9412) hydrogen bonds : bond 0.04179 / 3.06 ( 241) hydrogen bonds : angle 5.37612 / 3.87 ( 650) Misc. bond : bond 0.00075 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8762 (mt) cc_final: 0.8536 (mt) REVERT: A 764 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7595 (t70) REVERT: A 801 HIS cc_start: 0.8366 (t70) cc_final: 0.8126 (t-170) REVERT: A 812 LYS cc_start: 0.8700 (tppt) cc_final: 0.8425 (tppt) outliers start: 4 outliers final: 3 residues processed: 75 average time/residue: 0.1844 time to fit residues: 18.1671 Evaluate side-chains 72 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 764 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 24 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 4 optimal weight: 20.0000 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.146263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101634 restraints weight = 26756.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.107826 restraints weight = 12752.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111681 restraints weight = 8424.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113965 restraints weight = 6588.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.115333 restraints weight = 5671.838| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6801 Z= 0.144 Angle : 0.671 26.960 9412 Z= 0.305 Chirality : 0.071 1.921 1089 Planarity : 0.004 0.051 1062 Dihedral : 12.604 129.594 1274 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.83 % Allowed : 8.00 % Favored : 91.17 % 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 are not related in a simple way. whole: -2.08 (0.32), residues: 728 helix: 0.92 (0.36), residues: 222 sheet: -2.53 (0.38), residues: 169 loop : -2.36 (0.34), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 396 TYR 0.010 0.001 TYR A 376 PHE 0.013 0.001 PHE A 340 TRP 0.008 0.001 TRP A 569 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 6800) covalent geometry : angle 0.67063 / 0.31 ( 9412) hydrogen bonds : bond 0.03846 / 2.84 ( 241) hydrogen bonds : angle 5.14267 / 3.71 ( 650) Misc. bond : bond 0.00048 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8788 (mt) cc_final: 0.8578 (mt) REVERT: A 764 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7553 (t70) REVERT: A 801 HIS cc_start: 0.8358 (t70) cc_final: 0.8124 (t-170) outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.2310 time to fit residues: 21.8061 Evaluate side-chains 72 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 764 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 66 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 59 optimal weight: 0.6980 chunk 39 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 4 optimal weight: 30.0000 chunk 57 optimal weight: 5.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.102001 restraints weight = 26726.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.108201 restraints weight = 12737.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.112048 restraints weight = 8404.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114428 restraints weight = 6584.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115877 restraints weight = 5654.175| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6801 Z= 0.108 Angle : 0.652 26.851 9412 Z= 0.295 Chirality : 0.071 1.940 1089 Planarity : 0.004 0.050 1062 Dihedral : 12.493 131.519 1274 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.00 % Allowed : 8.50 % Favored : 90.50 % 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 are not related in a simple way. whole: -1.81 (0.32), residues: 728 helix: 1.09 (0.36), residues: 230 sheet: -2.31 (0.39), residues: 169 loop : -2.27 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 936 TYR 0.009 0.001 TYR A 376 PHE 0.009 0.001 PHE A 340 TRP 0.008 0.001 TRP A 569 HIS 0.003 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 6800) covalent geometry : angle 0.65201 / 0.30 ( 9412) hydrogen bonds : bond 0.03582 / 2.69 ( 241) hydrogen bonds : angle 4.92153 / 3.56 ( 650) Misc. bond : bond 0.00025 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 76 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 621 LEU cc_start: 0.8796 (mt) cc_final: 0.8582 (mt) REVERT: A 801 HIS cc_start: 0.8306 (t70) cc_final: 0.8091 (t-170) REVERT: A 802 GLU cc_start: 0.6324 (mt-10) cc_final: 0.6107 (mt-10) outliers start: 6 outliers final: 4 residues processed: 74 average time/residue: 0.2055 time to fit residues: 19.7177 Evaluate side-chains 71 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 67 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 30.0000 chunk 9 optimal weight: 50.0000 chunk 53 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 3 optimal weight: 30.0000 chunk 72 optimal weight: 8.9990 chunk 23 optimal weight: 20.0000 chunk 22 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 overall best weight: 6.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.143872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.099215 restraints weight = 26508.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.105039 restraints weight = 12863.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.108723 restraints weight = 8618.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111042 restraints weight = 6772.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112385 restraints weight = 5825.584| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 6801 Z= 0.241 Angle : 0.701 27.273 9412 Z= 0.324 Chirality : 0.072 1.912 1089 Planarity : 0.004 0.042 1062 Dihedral : 12.718 134.296 1274 Min Nonbonded Distance : 1.695 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 1.00 % Allowed : 9.83 % Favored : 89.17 % 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 are not related in a simple way. whole: -1.99 (0.32), residues: 728 helix: 0.92 (0.35), residues: 228 sheet: -2.42 (0.39), residues: 173 loop : -2.32 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 879 TYR 0.012 0.001 TYR A 357 PHE 0.018 0.001 PHE A 340 TRP 0.007 0.001 TRP A 605 HIS 0.004 0.001 HIS A 763 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.24 ( 6800) covalent geometry : angle 0.70058 / 0.32 ( 9412) hydrogen bonds : bond 0.03993 / 2.93 ( 241) hydrogen bonds : angle 5.08919 / 3.69 ( 650) Misc. bond : bond 0.00071 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 72 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7523 (mmp) cc_final: 0.6732 (mmp) REVERT: A 621 LEU cc_start: 0.8824 (mt) cc_final: 0.8621 (mt) REVERT: A 801 HIS cc_start: 0.8417 (t70) cc_final: 0.8201 (t-170) outliers start: 6 outliers final: 6 residues processed: 70 average time/residue: 0.2068 time to fit residues: 18.9916 Evaluate side-chains 71 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 487 HIS Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Chi-restraints excluded: chain A residue 830 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 56 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 13 optimal weight: 0.0470 chunk 7 optimal weight: 0.0870 chunk 51 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 1.8262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.146878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102048 restraints weight = 26215.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.108160 restraints weight = 12526.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112024 restraints weight = 8277.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114282 restraints weight = 6460.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.115732 restraints weight = 5589.192| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6801 Z= 0.103 Angle : 0.655 26.850 9412 Z= 0.298 Chirality : 0.071 1.942 1089 Planarity : 0.004 0.044 1062 Dihedral : 12.566 135.599 1274 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.67 % Allowed : 10.67 % Favored : 88.67 % 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 are not related in a simple way. whole: -1.72 (0.33), residues: 728 helix: 1.12 (0.36), residues: 230 sheet: -2.24 (0.39), residues: 169 loop : -2.20 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 936 TYR 0.009 0.001 TYR A 376 PHE 0.008 0.001 PHE A 340 TRP 0.008 0.001 TRP A 569 HIS 0.005 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 ( 6800) covalent geometry : angle 0.65484 / 0.30 ( 9412) hydrogen bonds : bond 0.03550 / 2.68 ( 241) hydrogen bonds : angle 4.85660 / 3.52 ( 650) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 73 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 69 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7540 (mmp) cc_final: 0.6729 (mmp) REVERT: A 801 HIS cc_start: 0.8327 (t70) cc_final: 0.8114 (t-170) outliers start: 4 outliers final: 4 residues processed: 70 average time/residue: 0.2058 time to fit residues: 18.8504 Evaluate side-chains 72 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 68 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 0.0980 chunk 59 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 10.0000 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.145060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100339 restraints weight = 26561.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.106386 restraints weight = 12745.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110080 restraints weight = 8430.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112386 restraints weight = 6628.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113584 restraints weight = 5717.769| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6801 Z= 0.183 Angle : 0.674 27.115 9412 Z= 0.308 Chirality : 0.072 1.928 1089 Planarity : 0.004 0.040 1062 Dihedral : 12.663 137.625 1274 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.67 % Allowed : 11.17 % Favored : 88.17 % 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 are not related in a simple way. whole: -1.78 (0.32), residues: 728 helix: 1.02 (0.35), residues: 230 sheet: -2.22 (0.39), residues: 171 loop : -2.21 (0.35), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 879 TYR 0.010 0.001 TYR A 376 PHE 0.016 0.001 PHE A 340 TRP 0.007 0.001 TRP A 569 HIS 0.004 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 6800) covalent geometry : angle 0.67377 / 0.31 ( 9412) hydrogen bonds : bond 0.03707 / 2.76 ( 241) hydrogen bonds : angle 4.91532 / 3.56 ( 650) Misc. bond : bond 0.00053 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 66 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7455 (mmp) cc_final: 0.6633 (mmp) REVERT: A 801 HIS cc_start: 0.8417 (t70) cc_final: 0.8208 (t-170) REVERT: A 802 GLU cc_start: 0.6552 (mt-10) cc_final: 0.6291 (mt-10) outliers start: 4 outliers final: 4 residues processed: 68 average time/residue: 0.2109 time to fit residues: 18.6377 Evaluate side-chains 69 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 44 optimal weight: 9.9990 chunk 12 optimal weight: 9.9990 chunk 70 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 38 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.146675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.101764 restraints weight = 26532.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.107948 restraints weight = 12687.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.111723 restraints weight = 8363.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.114069 restraints weight = 6557.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.115498 restraints weight = 5643.878| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6801 Z= 0.117 Angle : 0.654 26.968 9412 Z= 0.297 Chirality : 0.071 1.942 1089 Planarity : 0.004 0.040 1062 Dihedral : 12.567 139.231 1274 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.83 % Allowed : 11.17 % Favored : 88.00 % 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 are not related in a simple way. whole: -1.59 (0.33), residues: 728 helix: 1.17 (0.36), residues: 231 sheet: -2.01 (0.40), residues: 172 loop : -2.17 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 936 TYR 0.009 0.001 TYR A 376 PHE 0.010 0.001 PHE A 340 TRP 0.008 0.001 TRP A 569 HIS 0.003 0.001 HIS A 594 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 6800) covalent geometry : angle 0.65387 / 0.30 ( 9412) hydrogen bonds : bond 0.03461 / 2.64 ( 241) hydrogen bonds : angle 4.79789 / 3.47 ( 650) Misc. bond : bond 0.00025 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 435 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7480 (mmt) cc_final: 0.6699 (mmp) REVERT: A 584 ARG cc_start: 0.7955 (ttt180) cc_final: 0.7722 (ttp80) REVERT: A 802 GLU cc_start: 0.6362 (mt-10) cc_final: 0.6105 (mt-10) outliers start: 5 outliers final: 5 residues processed: 71 average time/residue: 0.2019 time to fit residues: 18.5418 Evaluate side-chains 72 residues out of total 660 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 407 LEU Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 564 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 46 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 15 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 32 optimal weight: 0.0470 chunk 51 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.146304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101608 restraints weight = 26442.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107746 restraints weight = 12686.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111509 restraints weight = 8382.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.113785 restraints weight = 6589.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.115191 restraints weight = 5676.030| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6801 Z= 0.132 Angle : 0.658 26.962 9412 Z= 0.298 Chirality : 0.072 1.944 1089 Planarity : 0.004 0.038 1062 Dihedral : 12.567 140.366 1274 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.67 % Allowed : 11.50 % Favored : 87.83 % 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 are not related in a simple way. whole: -1.58 (0.33), residues: 728 helix: 1.19 (0.36), residues: 231 sheet: -1.97 (0.40), residues: 174 loop : -2.19 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 936 TYR 0.009 0.001 TYR A 357 PHE 0.012 0.001 PHE A 340 TRP 0.007 0.001 TRP A 569 HIS 0.009 0.001 HIS A 801 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 ( 6800) covalent geometry : angle 0.65818 / 0.30 ( 9412) hydrogen bonds : bond 0.03430 / 2.60 ( 241) hydrogen bonds : angle 4.80452 / 3.48 ( 650) Misc. bond : bond 0.00036 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2182.98 seconds wall clock time: 37 minutes 52.65 seconds (2272.65 seconds total)