Starting phenix.real_space_refine on Sat Jul 20 11:03:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzb_42838/07_2024/8uzb_42838.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzb_42838/07_2024/8uzb_42838.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzb_42838/07_2024/8uzb_42838.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzb_42838/07_2024/8uzb_42838.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzb_42838/07_2024/8uzb_42838.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uzb_42838/07_2024/8uzb_42838.cif" } resolution = 2.63 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= 0.000 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 162 5.49 5 S 19 5.16 5 C 6286 2.51 5 N 1973 2.21 5 O 2442 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 84": "OE1" <-> "OE2" Residue "A ASP 112": "OD1" <-> "OD2" Residue "A GLU 289": "OE1" <-> "OE2" Residue "A ASP 337": "OD1" <-> "OD2" Residue "A ASP 510": "OD1" <-> "OD2" Residue "A ASP 723": "OD1" <-> "OD2" Residue "A TYR 790": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A TYR 864": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ASP 1017": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10882 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7485 Number of conformers: 1 Conformer: "" Number of residues, atoms: 910, 7485 Classifications: {'peptide': 910} Link IDs: {'PTRANS': 39, 'TRANS': 870} Chain breaks: 3 Chain: "B" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 2267 Classifications: {'RNA': 107} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 45, 'rna3p_pyr': 53} Link IDs: {'rna2p': 9, 'rna3p': 97} Chain breaks: 2 Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 808 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "D" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 322 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Time building chain proxies: 7.20, per 1000 atoms: 0.66 Number of scatterers: 10882 At special positions: 0 Unit cell: (97.65, 123.69, 132.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 19 16.00 P 162 15.00 O 2442 8.00 N 1973 7.00 C 6286 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.17 Conformation dependent library (CDL) restraints added in 1.5 seconds 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 45.1% alpha, 14.5% beta 68 base pairs and 109 stacking pairs defined. Time for finding SS restraints: 4.44 Creating SS restraints... Processing helix chain 'A' and resid 47 through 78 Processing helix chain 'A' and resid 81 through 89 removed outlier: 4.539A pdb=" N PHE A 89 " --> pdb=" O LEU A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 104 Processing helix chain 'A' and resid 110 through 124 removed outlier: 3.777A pdb=" N ARG A 124 " --> pdb=" O HIS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 removed outlier: 3.699A pdb=" N SER A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 168 through 171 Processing helix chain 'A' and resid 186 through 205 Processing helix chain 'A' and resid 210 through 222 Processing helix chain 'A' and resid 233 through 237 Processing helix chain 'A' and resid 253 through 268 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 299 through 306 Processing helix chain 'A' and resid 324 through 329 Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.184A pdb=" N SER A 356 " --> pdb=" O GLY A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 373 removed outlier: 3.534A pdb=" N PHE A 373 " --> pdb=" O ALA A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 383 Processing helix chain 'A' and resid 403 through 411 Processing helix chain 'A' and resid 422 through 434 Proline residue: A 431 - end of helix Processing helix chain 'A' and resid 438 through 447 Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 503 through 506 removed outlier: 4.097A pdb=" N SER A 506 " --> pdb=" O ARG A 503 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 503 through 506' Processing helix chain 'A' and resid 508 through 523 Processing helix chain 'A' and resid 667 through 679 Processing helix chain 'A' and resid 696 through 707 removed outlier: 3.816A pdb=" N THR A 700 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS A 702 " --> pdb=" O ARG A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 729 removed outlier: 3.673A pdb=" N VAL A 722 " --> pdb=" O LEU A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 748 removed outlier: 3.610A pdb=" N ILE A 735 " --> pdb=" O THR A 731 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA A 736 " --> pdb=" O PRO A 732 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LYS A 737 " --> pdb=" O SER A 733 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG A 744 " --> pdb=" O ALA A 740 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU A 746 " --> pdb=" O TYR A 742 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLN A 747 " --> pdb=" O GLN A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 774 removed outlier: 4.557A pdb=" N ARG A 771 " --> pdb=" O ALA A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 777 through 785 removed outlier: 3.502A pdb=" N LEU A 785 " --> pdb=" O SER A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 791 through 796 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 860 through 874 removed outlier: 3.565A pdb=" N TYR A 864 " --> pdb=" O ASP A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 877 through 882 Processing helix chain 'A' and resid 945 through 951 Processing helix chain 'A' and resid 963 through 967 Processing sheet with id=AA1, first strand: chain 'A' and resid 692 through 694 removed outlier: 6.286A pdb=" N ILE A 497 " --> pdb=" O TYR A 693 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N VAL A 14 " --> pdb=" O VAL A 31 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N VAL A 31 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TRP A 16 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N LEU A 29 " --> pdb=" O TRP A 16 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL A 18 " --> pdb=" O GLU A 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 276 through 278 Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298 removed outlier: 6.784A pdb=" N ILE A 297 " --> pdb=" O PHE A 333 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 388 removed outlier: 4.110A pdb=" N TYR A 387 " --> pdb=" O MET A 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 826 removed outlier: 5.818A pdb=" N TYR A 823 " --> pdb=" O VAL A 836 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL A 836 " --> pdb=" O TYR A 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 887 through 889 Processing sheet with id=AA7, first strand: chain 'A' and resid 911 through 914 removed outlier: 4.370A pdb=" N THR A 919 " --> pdb=" O LEU A 914 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 937 through 944 removed outlier: 6.394A pdb=" N VAL A 929 " --> pdb=" O SER A 979 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N SER A 979 " --> pdb=" O VAL A 929 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 931 " --> pdb=" O ARG A 977 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 956 through 957 removed outlier: 3.843A pdb=" N LYS A 968 " --> pdb=" O ALA A 957 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1033 through 1038 removed outlier: 5.318A pdb=" N LEU A1023 " --> pdb=" O GLY A1036 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A1015 " --> pdb=" O GLU A1024 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ILE A1026 " --> pdb=" O TYR A1013 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N TYR A1013 " --> pdb=" O ILE A1026 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP A1008 " --> pdb=" O ARG A 992 " (cutoff:3.500A) removed outlier: 11.580A pdb=" N ARG A 992 " --> pdb=" O ASP A1008 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N PHE A1010 " --> pdb=" O LEU A 990 " (cutoff:3.500A) removed outlier: 11.298A pdb=" N LEU A 990 " --> pdb=" O PHE A1010 " (cutoff:3.500A) removed outlier: 9.940A pdb=" N TYR A1012 " --> pdb=" O ILE A 988 " (cutoff:3.500A) removed outlier: 9.830A pdb=" N ILE A 988 " --> pdb=" O TYR A1012 " (cutoff:3.500A) removed outlier: 9.883A pdb=" N LYS A1014 " --> pdb=" O ILE A 986 " (cutoff:3.500A) removed outlier: 11.406A pdb=" N ILE A 986 " --> pdb=" O LYS A1014 " (cutoff:3.500A) removed outlier: 11.110A pdb=" N ILE A1016 " --> pdb=" O ASP A 984 " (cutoff:3.500A) removed outlier: 13.412A pdb=" N ASP A 984 " --> pdb=" O ILE A1016 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 985 " --> pdb=" O TYR A1048 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG A1044 " --> pdb=" O GLU A 989 " (cutoff:3.500A) 309 hydrogen bonds defined for protein. 888 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 171 hydrogen bonds 326 hydrogen bond angles 0 basepair planarities 68 basepair parallelities 109 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2908 1.34 - 1.46: 2984 1.46 - 1.58: 5187 1.58 - 1.70: 319 1.70 - 1.82: 33 Bond restraints: 11431 Sorted by residual: bond pdb=" CB PRO A 778 " pdb=" CG PRO A 778 " ideal model delta sigma weight residual 1.492 1.567 -0.075 5.00e-02 4.00e+02 2.24e+00 bond pdb=" C3' DG C 16 " pdb=" O3' DG C 16 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.69e+00 bond pdb=" C3' C B 77 " pdb=" O3' C B 77 " ideal model delta sigma weight residual 1.427 1.442 -0.015 1.50e-02 4.44e+03 1.03e+00 bond pdb=" CG PRO A 778 " pdb=" CD PRO A 778 " ideal model delta sigma weight residual 1.503 1.470 0.033 3.40e-02 8.65e+02 9.58e-01 bond pdb=" CA THR A 416 " pdb=" CB THR A 416 " ideal model delta sigma weight residual 1.521 1.535 -0.014 1.48e-02 4.57e+03 9.16e-01 ... (remaining 11426 not shown) Histogram of bond angle deviations from ideal: 97.57 - 104.87: 796 104.87 - 112.17: 5941 112.17 - 119.47: 3847 119.47 - 126.77: 5067 126.77 - 134.06: 499 Bond angle restraints: 16150 Sorted by residual: angle pdb=" C THR A 416 " pdb=" N LYS A 417 " pdb=" CA LYS A 417 " ideal model delta sigma weight residual 121.91 128.69 -6.78 2.03e+00 2.43e-01 1.11e+01 angle pdb=" C3' C B 77 " pdb=" O3' C B 77 " pdb=" P A B 78 " ideal model delta sigma weight residual 120.20 124.88 -4.68 1.50e+00 4.44e-01 9.75e+00 angle pdb=" N THR A 416 " pdb=" CA THR A 416 " pdb=" C THR A 416 " ideal model delta sigma weight residual 107.20 111.47 -4.27 1.70e+00 3.46e-01 6.32e+00 angle pdb=" CB MET A 207 " pdb=" CG MET A 207 " pdb=" SD MET A 207 " ideal model delta sigma weight residual 112.70 120.01 -7.31 3.00e+00 1.11e-01 5.94e+00 angle pdb=" N PRO A 778 " pdb=" CD PRO A 778 " pdb=" CG PRO A 778 " ideal model delta sigma weight residual 103.20 99.67 3.53 1.50e+00 4.44e-01 5.53e+00 ... (remaining 16145 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.01: 6437 33.01 - 66.02: 539 66.02 - 99.03: 41 99.03 - 132.04: 0 132.04 - 165.05: 3 Dihedral angle restraints: 7020 sinusoidal: 4348 harmonic: 2672 Sorted by residual: dihedral pdb=" C4' DT C 6 " pdb=" C3' DT C 6 " pdb=" O3' DT C 6 " pdb=" P DG C 7 " ideal model delta sinusoidal sigma weight residual 220.00 54.95 165.05 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' C B 77 " pdb=" C3' C B 77 " pdb=" O3' C B 77 " pdb=" P A B 78 " ideal model delta sinusoidal sigma weight residual -110.00 55.03 -165.03 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG C 16 " pdb=" C3' DG C 16 " pdb=" O3' DG C 16 " pdb=" P DG C 17 " ideal model delta sinusoidal sigma weight residual 220.00 61.09 158.91 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 7017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1417 0.038 - 0.075: 329 0.075 - 0.113: 85 0.113 - 0.150: 20 0.150 - 0.188: 3 Chirality restraints: 1854 Sorted by residual: chirality pdb=" C3' C B 77 " pdb=" C4' C B 77 " pdb=" O3' C B 77 " pdb=" C2' C B 77 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.83e-01 chirality pdb=" CB THR A 416 " pdb=" CA THR A 416 " pdb=" OG1 THR A 416 " pdb=" CG2 THR A 416 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.69e-01 chirality pdb=" CA TRP A 763 " pdb=" N TRP A 763 " pdb=" C TRP A 763 " pdb=" CB TRP A 763 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.99e-01 ... (remaining 1851 not shown) Planarity restraints: 1494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 777 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO A 778 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 778 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 778 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT C 13 " 0.024 2.00e-02 2.50e+03 1.18e-02 3.50e+00 pdb=" N1 DT C 13 " -0.027 2.00e-02 2.50e+03 pdb=" C2 DT C 13 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT C 13 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DT C 13 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT C 13 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT C 13 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT C 13 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT C 13 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DT C 13 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 93 " -0.020 2.00e-02 2.50e+03 8.95e-03 2.40e+00 pdb=" N9 G B 93 " 0.023 2.00e-02 2.50e+03 pdb=" C8 G B 93 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 93 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G B 93 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G B 93 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G B 93 " -0.006 2.00e-02 2.50e+03 pdb=" N1 G B 93 " -0.001 2.00e-02 2.50e+03 pdb=" C2 G B 93 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 93 " 0.003 2.00e-02 2.50e+03 pdb=" N3 G B 93 " 0.001 2.00e-02 2.50e+03 pdb=" C4 G B 93 " 0.001 2.00e-02 2.50e+03 ... (remaining 1491 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 396 2.70 - 3.25: 9681 3.25 - 3.80: 19056 3.80 - 4.35: 25439 4.35 - 4.90: 37296 Nonbonded interactions: 91868 Sorted by model distance: nonbonded pdb=" OG SER A 381 " pdb=" O GLU A 386 " model vdw 2.147 2.440 nonbonded pdb=" OG1 THR A 12 " pdb=" O PHE A 34 " model vdw 2.214 2.440 nonbonded pdb=" OD1 ASP A 768 " pdb=" NH2 ARG A 771 " model vdw 2.233 2.520 nonbonded pdb=" OD1 ASP A 337 " pdb=" NE2 GLN A 341 " model vdw 2.243 2.520 nonbonded pdb=" OD2 ASP A 28 " pdb=" OH TYR A 491 " model vdw 2.254 2.440 ... (remaining 91863 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.700 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:11.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 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 : 0.003 0.075 11431 Z= 0.194 Angle : 0.528 7.309 16150 Z= 0.284 Chirality : 0.037 0.188 1854 Planarity : 0.004 0.062 1494 Dihedral : 20.256 165.051 5292 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.28), residues: 902 helix: 1.28 (0.27), residues: 375 sheet: -0.76 (0.47), residues: 120 loop : -0.12 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 763 HIS 0.002 0.001 HIS A1028 PHE 0.009 0.001 PHE A 759 TYR 0.020 0.001 TYR A 864 ARG 0.007 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.930 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 1.5883 time to fit residues: 180.5510 Evaluate side-chains 80 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 1.9990 chunk 79 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 53 optimal weight: 0.1980 chunk 42 optimal weight: 0.0030 chunk 82 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.0912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11431 Z= 0.204 Angle : 0.528 6.576 16150 Z= 0.284 Chirality : 0.037 0.182 1854 Planarity : 0.004 0.034 1494 Dihedral : 22.157 165.707 3337 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.97 % Allowed : 9.25 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.29), residues: 902 helix: 1.60 (0.27), residues: 387 sheet: -0.74 (0.44), residues: 131 loop : -0.08 (0.32), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 763 HIS 0.003 0.001 HIS A1028 PHE 0.010 0.001 PHE A 932 TYR 0.007 0.001 TYR A 491 ARG 0.005 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 89 time to evaluate : 1.024 Fit side-chains REVERT: A 335 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7337 (mt-10) REVERT: A 337 ASP cc_start: 0.7935 (t70) cc_final: 0.7592 (t0) outliers start: 16 outliers final: 6 residues processed: 98 average time/residue: 1.5756 time to fit residues: 164.6839 Evaluate side-chains 86 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 795 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 95 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1005 ASN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 11431 Z= 0.412 Angle : 0.651 7.381 16150 Z= 0.347 Chirality : 0.044 0.198 1854 Planarity : 0.006 0.046 1494 Dihedral : 22.383 168.068 3337 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.58 % Allowed : 9.86 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.28), residues: 902 helix: 1.29 (0.27), residues: 386 sheet: -0.93 (0.42), residues: 134 loop : -0.43 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 763 HIS 0.008 0.001 HIS A1028 PHE 0.017 0.002 PHE A 932 TYR 0.012 0.002 TYR A 864 ARG 0.008 0.001 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 93 time to evaluate : 1.007 Fit side-chains REVERT: A 335 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7410 (mt-10) REVERT: A 337 ASP cc_start: 0.7926 (t70) cc_final: 0.7565 (t0) REVERT: A 500 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: A 869 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7577 (mm-40) REVERT: A 948 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8583 (mt) REVERT: A 1044 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.7705 (ttm-80) outliers start: 29 outliers final: 12 residues processed: 110 average time/residue: 1.6859 time to fit residues: 197.0390 Evaluate side-chains 99 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 513 ARG Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 94 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11431 Z= 0.165 Angle : 0.514 6.319 16150 Z= 0.277 Chirality : 0.037 0.191 1854 Planarity : 0.004 0.035 1494 Dihedral : 22.106 164.948 3337 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.10 % Allowed : 13.56 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.28), residues: 902 helix: 1.72 (0.27), residues: 389 sheet: -1.20 (0.43), residues: 122 loop : -0.09 (0.32), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 763 HIS 0.002 0.001 HIS A1028 PHE 0.008 0.001 PHE A 759 TYR 0.012 0.001 TYR A 864 ARG 0.007 0.000 ARG A1060 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 1.063 Fit side-chains REVERT: A 28 ASP cc_start: 0.7965 (m-30) cc_final: 0.7752 (m-30) REVERT: A 162 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.7043 (tp30) REVERT: A 337 ASP cc_start: 0.7802 (t70) cc_final: 0.7453 (t0) outliers start: 17 outliers final: 6 residues processed: 105 average time/residue: 1.5482 time to fit residues: 173.0725 Evaluate side-chains 89 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 84 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 0.6980 chunk 41 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 0 optimal weight: 0.9980 chunk 51 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11431 Z= 0.236 Angle : 0.538 6.291 16150 Z= 0.290 Chirality : 0.038 0.179 1854 Planarity : 0.004 0.033 1494 Dihedral : 22.147 165.935 3337 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.70 % Allowed : 13.07 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.28), residues: 902 helix: 1.71 (0.27), residues: 389 sheet: -1.16 (0.42), residues: 127 loop : -0.11 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 763 HIS 0.003 0.001 HIS A1028 PHE 0.013 0.001 PHE A 932 TYR 0.014 0.001 TYR A 864 ARG 0.007 0.000 ARG A1060 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 87 time to evaluate : 1.071 Fit side-chains REVERT: A 29 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7997 (mp) REVERT: A 38 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: A 162 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6979 (tp30) REVERT: A 335 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7342 (mt-10) REVERT: A 337 ASP cc_start: 0.7844 (t70) cc_final: 0.7486 (t0) REVERT: A 500 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7436 (tt0) REVERT: A 706 ARG cc_start: 0.7343 (OUTLIER) cc_final: 0.6986 (mmt90) REVERT: A 789 ASN cc_start: 0.7926 (OUTLIER) cc_final: 0.7636 (p0) REVERT: A 869 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7626 (mm-40) REVERT: A 948 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8403 (mt) REVERT: A 966 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7163 (mt-10) outliers start: 30 outliers final: 10 residues processed: 108 average time/residue: 1.6223 time to fit residues: 186.2410 Evaluate side-chains 101 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 81 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 695 VAL Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 ARG Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 34 optimal weight: 4.9990 chunk 91 optimal weight: 8.9990 chunk 20 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 25 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 793 GLN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11431 Z= 0.394 Angle : 0.634 8.389 16150 Z= 0.339 Chirality : 0.043 0.178 1854 Planarity : 0.006 0.045 1494 Dihedral : 22.323 167.776 3337 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.44 % Allowed : 13.56 % Favored : 82.00 % 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: 0.35 (0.28), residues: 902 helix: 1.38 (0.27), residues: 388 sheet: -1.16 (0.43), residues: 124 loop : -0.38 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 763 HIS 0.005 0.001 HIS A1028 PHE 0.019 0.002 PHE A 932 TYR 0.017 0.002 TYR A 864 ARG 0.007 0.001 ARG A1060 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 82 time to evaluate : 1.050 Fit side-chains REVERT: A 29 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8178 (mp) REVERT: A 290 GLN cc_start: 0.6909 (mt0) cc_final: 0.6449 (mm-40) REVERT: A 335 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7347 (mt-10) REVERT: A 337 ASP cc_start: 0.7909 (t70) cc_final: 0.7546 (t0) REVERT: A 500 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7471 (tt0) REVERT: A 706 ARG cc_start: 0.7334 (OUTLIER) cc_final: 0.6896 (mmt90) REVERT: A 869 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7555 (mm-40) REVERT: A 948 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8506 (mt) REVERT: A 966 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: A 1044 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7628 (ttm-80) outliers start: 36 outliers final: 11 residues processed: 104 average time/residue: 1.6135 time to fit residues: 178.8294 Evaluate side-chains 100 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ILE Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 335 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 ARG Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 97 optimal weight: 7.9990 chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11431 Z= 0.218 Angle : 0.536 6.389 16150 Z= 0.289 Chirality : 0.038 0.178 1854 Planarity : 0.004 0.032 1494 Dihedral : 22.154 165.314 3337 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.33 % Allowed : 14.80 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.28), residues: 902 helix: 1.67 (0.27), residues: 389 sheet: -1.20 (0.43), residues: 127 loop : -0.22 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 763 HIS 0.003 0.001 HIS A1028 PHE 0.010 0.001 PHE A 932 TYR 0.013 0.001 TYR A 864 ARG 0.008 0.000 ARG A1060 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 85 time to evaluate : 1.038 Fit side-chains REVERT: A 38 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7851 (pt0) REVERT: A 290 GLN cc_start: 0.6816 (mt0) cc_final: 0.6597 (mm-40) REVERT: A 337 ASP cc_start: 0.7808 (t70) cc_final: 0.7450 (t0) REVERT: A 706 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.6856 (mmt90) REVERT: A 789 ASN cc_start: 0.7725 (OUTLIER) cc_final: 0.7525 (p0) REVERT: A 869 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7628 (mm-40) REVERT: A 948 ILE cc_start: 0.8659 (OUTLIER) cc_final: 0.8354 (mt) REVERT: A 966 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: A 1044 ARG cc_start: 0.8259 (OUTLIER) cc_final: 0.7618 (ttm-80) outliers start: 27 outliers final: 12 residues processed: 105 average time/residue: 1.5685 time to fit residues: 175.2143 Evaluate side-chains 99 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 ARG Chi-restraints excluded: chain A residue 789 ASN Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 40 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.0670 chunk 79 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 overall best weight: 1.3722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11431 Z= 0.220 Angle : 0.539 7.113 16150 Z= 0.288 Chirality : 0.038 0.178 1854 Planarity : 0.004 0.032 1494 Dihedral : 22.136 165.525 3337 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.45 % Allowed : 14.67 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.28), residues: 902 helix: 1.77 (0.27), residues: 388 sheet: -1.21 (0.43), residues: 127 loop : -0.22 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 763 HIS 0.004 0.001 HIS A1028 PHE 0.010 0.001 PHE A 932 TYR 0.016 0.001 TYR A 864 ARG 0.002 0.000 ARG A1040 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 1.012 Fit side-chains REVERT: A 38 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7864 (pt0) REVERT: A 337 ASP cc_start: 0.7815 (t70) cc_final: 0.7476 (t0) REVERT: A 706 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.6854 (mmt90) REVERT: A 869 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7634 (mm-40) REVERT: A 948 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8366 (mt) REVERT: A 966 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: A 1044 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7623 (ttm-80) outliers start: 28 outliers final: 15 residues processed: 106 average time/residue: 1.5240 time to fit residues: 172.2041 Evaluate side-chains 102 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 81 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 ARG Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1003 GLU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 56 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 89 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 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 290 GLN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 11431 Z= 0.363 Angle : 0.624 9.364 16150 Z= 0.332 Chirality : 0.043 0.178 1854 Planarity : 0.005 0.044 1494 Dihedral : 22.283 167.010 3337 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.08 % Allowed : 15.41 % Favored : 81.50 % 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: 0.37 (0.28), residues: 902 helix: 1.45 (0.27), residues: 389 sheet: -1.21 (0.42), residues: 124 loop : -0.40 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 763 HIS 0.005 0.001 HIS A1028 PHE 0.017 0.002 PHE A 932 TYR 0.020 0.002 TYR A 864 ARG 0.004 0.001 ARG A1040 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 1.017 Fit side-chains REVERT: A 38 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: A 143 MET cc_start: 0.6882 (OUTLIER) cc_final: 0.5822 (ttp) REVERT: A 337 ASP cc_start: 0.7880 (t70) cc_final: 0.7527 (t0) REVERT: A 706 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6875 (mmt90) REVERT: A 869 GLN cc_start: 0.7937 (OUTLIER) cc_final: 0.7594 (mm-40) REVERT: A 948 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8506 (mt) REVERT: A 966 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7172 (mt-10) REVERT: A 1044 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7628 (ttm-80) outliers start: 25 outliers final: 15 residues processed: 99 average time/residue: 1.5470 time to fit residues: 162.9779 Evaluate side-chains 103 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 143 MET Chi-restraints excluded: chain A residue 144 LEU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 290 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 666 THR Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 ARG Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 966 GLU Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 99 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 69 optimal weight: 0.3980 chunk 104 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 51 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 789 ASN ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11431 Z= 0.172 Angle : 0.522 6.352 16150 Z= 0.279 Chirality : 0.036 0.178 1854 Planarity : 0.004 0.034 1494 Dihedral : 22.089 164.570 3337 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.22 % Allowed : 16.03 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.28), residues: 902 helix: 1.81 (0.27), residues: 389 sheet: -1.15 (0.43), residues: 127 loop : -0.18 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 763 HIS 0.003 0.001 HIS A1028 PHE 0.007 0.001 PHE A 759 TYR 0.015 0.001 TYR A 864 ARG 0.002 0.000 ARG A 63 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1804 Ramachandran restraints generated. 902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.052 Fit side-chains REVERT: A 38 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7798 (pt0) REVERT: A 162 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7048 (tp30) REVERT: A 337 ASP cc_start: 0.7749 (t70) cc_final: 0.7415 (t0) REVERT: A 706 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6849 (mmt90) REVERT: A 869 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.7616 (mm-40) REVERT: A 948 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8217 (mt) REVERT: A 1031 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7292 (ttm-80) REVERT: A 1044 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7617 (ttm-80) outliers start: 18 outliers final: 9 residues processed: 93 average time/residue: 1.6341 time to fit residues: 162.1577 Evaluate side-chains 92 residues out of total 811 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 1.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLU Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 280 THR Chi-restraints excluded: chain A residue 285 ARG Chi-restraints excluded: chain A residue 670 SER Chi-restraints excluded: chain A residue 686 SER Chi-restraints excluded: chain A residue 705 SER Chi-restraints excluded: chain A residue 706 ARG Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain A residue 869 GLN Chi-restraints excluded: chain A residue 948 ILE Chi-restraints excluded: chain A residue 1044 ARG Chi-restraints excluded: chain A residue 1046 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 88 optimal weight: 2.9990 chunk 25 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 23 optimal weight: 0.0870 chunk 83 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 73 optimal weight: 0.6980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 GLN ** A 385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.135573 restraints weight = 11160.301| |-----------------------------------------------------------------------------| r_work (start): 0.3578 rms_B_bonded: 2.01 r_work: 0.3266 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11431 Z= 0.153 Angle : 0.498 8.608 16150 Z= 0.265 Chirality : 0.035 0.178 1854 Planarity : 0.003 0.035 1494 Dihedral : 22.026 165.276 3337 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.22 % Allowed : 16.40 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.28), residues: 902 helix: 2.02 (0.27), residues: 389 sheet: -1.22 (0.43), residues: 121 loop : -0.02 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 763 HIS 0.006 0.001 HIS A1028 PHE 0.007 0.001 PHE A 127 TYR 0.015 0.001 TYR A 864 ARG 0.002 0.000 ARG A 63 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3691.90 seconds wall clock time: 65 minutes 21.76 seconds (3921.76 seconds total)