Starting phenix.real_space_refine on Thu Sep 26 07:16:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/09_2024/7kx9_23063.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/09_2024/7kx9_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/09_2024/7kx9_23063.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/09_2024/7kx9_23063.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/09_2024/7kx9_23063.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kx9_23063/09_2024/7kx9_23063.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 5} 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: 6.14, per 1000 atoms: 0.49 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: 3.40 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 5.89 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: 4.08 Time building geometry restraints manager: 3.93 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: 5570 24.09 - 48.19: 330 48.19 - 72.28: 87 72.28 - 96.37: 19 96.37 - 120.47: 4 Dihedral angle restraints: 6010 sinusoidal: 3505 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 6007 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: 0.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.230 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.150 Process input model: 33.880 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 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 : 0.008 0.170 6800 Z= 0.513 Angle : 0.934 27.403 9412 Z= 0.453 Chirality : 0.074 1.921 1089 Planarity : 0.005 0.044 1062 Dihedral : 17.248 120.468 2747 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 12.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.006 0.001 TRP A 623 HIS 0.009 0.001 HIS A 487 PHE 0.009 0.001 PHE A 340 TYR 0.011 0.002 TYR A 435 ARG 0.010 0.001 ARG A 629 *********************** 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 fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 1.005 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: 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: 0.4607 time to fit residues: 52.0217 Evaluate side-chains 68 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.952 ------------------------------------------------------------------------------- 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 64 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 31 optimal weight: 9.9990 chunk 19 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 59 optimal weight: 0.0770 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 69 optimal weight: 0.5980 overall best weight: 2.9342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 594 HIS A 640 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6800 Z= 0.231 Angle : 0.752 27.242 9412 Z= 0.351 Chirality : 0.071 1.899 1089 Planarity : 0.005 0.085 1062 Dihedral : 17.567 116.421 1402 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.17 % Allowed : 5.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.30), residues: 728 helix: -0.01 (0.34), residues: 220 sheet: -2.92 (0.37), residues: 171 loop : -2.66 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.005 0.001 HIS A 458 PHE 0.015 0.001 PHE A 406 TYR 0.011 0.001 TYR A 376 ARG 0.007 0.001 ARG A 671 *********************** 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 76 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7280 (mmp) cc_final: 0.6790 (mmp) REVERT: A 621 LEU cc_start: 0.8640 (mt) cc_final: 0.8434 (mt) REVERT: A 793 GLN cc_start: 0.6629 (mp10) cc_final: 0.4475 (mp10) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.4094 time to fit residues: 39.6906 Evaluate side-chains 70 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 8.9990 chunk 21 optimal weight: 40.0000 chunk 57 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 69 optimal weight: 6.9990 chunk 74 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 882 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6800 Z= 0.271 Angle : 0.708 26.959 9412 Z= 0.329 Chirality : 0.072 1.918 1089 Planarity : 0.004 0.054 1062 Dihedral : 17.524 126.054 1400 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.33 % Allowed : 6.67 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.31), residues: 728 helix: 0.42 (0.35), residues: 221 sheet: -2.86 (0.36), residues: 175 loop : -2.56 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 569 HIS 0.013 0.001 HIS A 763 PHE 0.015 0.001 PHE A 340 TYR 0.011 0.001 TYR A 376 ARG 0.003 0.000 ARG A 671 *********************** 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 79 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ILE cc_start: 0.9217 (pt) cc_final: 0.8976 (mt) REVERT: A 621 LEU cc_start: 0.8678 (mt) cc_final: 0.8467 (mt) REVERT: A 801 HIS cc_start: 0.8309 (t70) cc_final: 0.8081 (t-170) outliers start: 2 outliers final: 2 residues processed: 77 average time/residue: 0.4530 time to fit residues: 44.8339 Evaluate side-chains 72 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 528 PHE Chi-restraints excluded: chain A residue 812 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 19 optimal weight: 8.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6800 Z= 0.192 Angle : 0.679 26.814 9412 Z= 0.311 Chirality : 0.071 1.929 1089 Planarity : 0.004 0.048 1062 Dihedral : 17.395 125.541 1400 Min Nonbonded Distance : 1.754 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 0.67 % Allowed : 7.50 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.31), residues: 728 helix: 0.71 (0.35), residues: 222 sheet: -2.59 (0.38), residues: 169 loop : -2.39 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 569 HIS 0.003 0.001 HIS A 763 PHE 0.012 0.001 PHE A 340 TYR 0.010 0.001 TYR A 376 ARG 0.003 0.000 ARG A 671 *********************** 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 82 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 ILE cc_start: 0.9212 (pt) cc_final: 0.8959 (mt) REVERT: A 801 HIS cc_start: 0.8261 (t70) cc_final: 0.8056 (t-170) outliers start: 4 outliers final: 3 residues processed: 79 average time/residue: 0.4905 time to fit residues: 49.8392 Evaluate side-chains 75 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.937 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 8.9990 chunk 41 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6800 Z= 0.298 Angle : 0.690 26.972 9412 Z= 0.318 Chirality : 0.072 1.924 1089 Planarity : 0.004 0.048 1062 Dihedral : 17.435 129.485 1400 Min Nonbonded Distance : 1.714 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.67 % Allowed : 9.00 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.32), residues: 728 helix: 0.78 (0.35), residues: 222 sheet: -2.59 (0.37), residues: 175 loop : -2.34 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 569 HIS 0.005 0.001 HIS A 763 PHE 0.015 0.001 PHE A 340 TYR 0.011 0.001 TYR A 376 ARG 0.004 0.000 ARG A 936 *********************** 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 78 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 HIS cc_start: 0.8351 (t70) cc_final: 0.8130 (t-170) outliers start: 4 outliers final: 4 residues processed: 76 average time/residue: 0.4560 time to fit residues: 44.6360 Evaluate side-chains 75 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 24 optimal weight: 20.0000 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 73 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 6800 Z= 0.164 Angle : 0.659 26.803 9412 Z= 0.300 Chirality : 0.071 1.943 1089 Planarity : 0.004 0.042 1062 Dihedral : 17.319 130.546 1400 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 0.83 % Allowed : 10.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.32), residues: 728 helix: 0.96 (0.36), residues: 224 sheet: -2.39 (0.38), residues: 171 loop : -2.23 (0.35), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.003 0.001 HIS A 763 PHE 0.009 0.001 PHE A 340 TYR 0.009 0.001 TYR A 376 ARG 0.003 0.000 ARG A 936 *********************** 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 78 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 73 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 HIS cc_start: 0.8283 (t70) cc_final: 0.8078 (t-170) outliers start: 5 outliers final: 4 residues processed: 75 average time/residue: 0.4497 time to fit residues: 43.5922 Evaluate side-chains 73 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 8 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 22 optimal weight: 30.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6800 Z= 0.181 Angle : 0.650 26.762 9412 Z= 0.295 Chirality : 0.072 1.957 1089 Planarity : 0.004 0.038 1062 Dihedral : 17.200 133.674 1400 Min Nonbonded Distance : 1.770 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 0.67 % Allowed : 10.83 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.33), residues: 728 helix: 1.12 (0.36), residues: 230 sheet: -2.11 (0.39), residues: 174 loop : -2.19 (0.36), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.003 0.000 HIS A 763 PHE 0.011 0.001 PHE A 340 TYR 0.010 0.001 TYR A 435 ARG 0.003 0.000 ARG A 936 *********************** 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 73 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.920 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 71 average time/residue: 0.4770 time to fit residues: 43.5758 Evaluate side-chains 71 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 14 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 49 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 64 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6800 Z= 0.170 Angle : 0.644 26.815 9412 Z= 0.292 Chirality : 0.072 1.962 1089 Planarity : 0.004 0.045 1062 Dihedral : 17.128 136.318 1400 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.83 % Allowed : 10.67 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.33), residues: 728 helix: 1.26 (0.36), residues: 230 sheet: -2.13 (0.39), residues: 169 loop : -2.13 (0.35), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.009 0.001 HIS A 801 PHE 0.010 0.001 PHE A 340 TYR 0.008 0.001 TYR A 376 ARG 0.005 0.000 ARG A 396 *********************** 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 76 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 71 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 73 average time/residue: 0.4947 time to fit residues: 46.0511 Evaluate side-chains 73 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 69 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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 29 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 72 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 75 optimal weight: 30.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6800 Z= 0.277 Angle : 0.666 27.013 9412 Z= 0.304 Chirality : 0.072 1.946 1089 Planarity : 0.004 0.035 1062 Dihedral : 17.169 138.674 1400 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.00 % Allowed : 10.50 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.33), residues: 728 helix: 1.23 (0.35), residues: 228 sheet: -2.08 (0.40), residues: 174 loop : -2.20 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 569 HIS 0.008 0.001 HIS A 801 PHE 0.016 0.001 PHE A 340 TYR 0.009 0.001 TYR A 376 ARG 0.005 0.000 ARG A 396 *********************** 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 74 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 398 MET cc_start: 0.7670 (mmt) cc_final: 0.7192 (mmp) outliers start: 6 outliers final: 6 residues processed: 71 average time/residue: 0.4891 time to fit residues: 44.5013 Evaluate side-chains 74 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LYS 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 830 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 69 optimal weight: 5.9990 chunk 60 optimal weight: 0.0870 chunk 6 optimal weight: 0.0270 chunk 46 optimal weight: 3.9990 chunk 36 optimal weight: 9.9990 chunk 47 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.2983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6800 Z= 0.147 Angle : 0.641 26.809 9412 Z= 0.291 Chirality : 0.072 1.966 1089 Planarity : 0.004 0.037 1062 Dihedral : 17.076 140.503 1400 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.00 % Allowed : 10.50 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.33), residues: 728 helix: 1.38 (0.36), residues: 231 sheet: -1.92 (0.40), residues: 174 loop : -2.09 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 569 HIS 0.006 0.001 HIS A 801 PHE 0.008 0.001 PHE A 340 TYR 0.007 0.001 TYR A 376 ARG 0.004 0.000 ARG A 396 ********************** 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 80 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 74 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 75 average time/residue: 0.4800 time to fit residues: 46.1008 Evaluate side-chains 74 residues out of total 660 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 LYS 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 60 optimal weight: 4.9990 chunk 25 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 458 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 908 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.147325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102507 restraints weight = 26559.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108658 restraints weight = 12645.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112474 restraints weight = 8375.351| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6800 Z= 0.201 Angle : 0.642 26.910 9412 Z= 0.290 Chirality : 0.072 1.964 1089 Planarity : 0.004 0.035 1062 Dihedral : 17.054 141.941 1400 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 1.00 % Allowed : 10.67 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.33), residues: 728 helix: 1.37 (0.36), residues: 231 sheet: -1.93 (0.40), residues: 174 loop : -2.10 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 373 HIS 0.007 0.001 HIS A 801 PHE 0.012 0.001 PHE A 340 TYR 0.008 0.001 TYR A 376 ARG 0.004 0.000 ARG A 396 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2971.88 seconds wall clock time: 54 minutes 24.42 seconds (3264.42 seconds total)