Starting phenix.real_space_refine on Tue Feb 13 13:11:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfx_33800/02_2024/7yfx_33800_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfx_33800/02_2024/7yfx_33800.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfx_33800/02_2024/7yfx_33800_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfx_33800/02_2024/7yfx_33800_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfx_33800/02_2024/7yfx_33800_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfx_33800/02_2024/7yfx_33800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfx_33800/02_2024/7yfx_33800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfx_33800/02_2024/7yfx_33800_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yfx_33800/02_2024/7yfx_33800_updated.pdb" } resolution = 3.4 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= -0.002 sd= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 15 5.49 5 Mg 2 5.21 5 S 47 5.16 5 C 3989 2.51 5 N 1096 2.21 5 O 1170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 290": "OE1" <-> "OE2" Residue "A GLU 313": "OE1" <-> "OE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 543": "OE1" <-> "OE2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A GLU 643": "OE1" <-> "OE2" Residue "A GLU 650": "OE1" <-> "OE2" Residue "A GLU 968": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6319 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 5999 Classifications: {'peptide': 746} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 38, 'TRANS': 707} Chain breaks: 1 Chain: "B" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'RNA': 15} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 1, 'rna2p_pyr': 3, 'rna3p_pur': 6, 'rna3p_pyr': 4} Link IDs: {'rna2p': 4, 'rna3p': 10} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.11, per 1000 atoms: 0.65 Number of scatterers: 6319 At special positions: 0 Unit cell: (84.0294, 115.271, 89.4159, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 47 16.00 P 15 15.00 Mg 2 11.99 O 1170 8.00 N 1096 7.00 C 3989 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: 3.03 Conformation dependent library (CDL) restraints added in 1.1 seconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 22 helices and 9 sheets defined 33.0% alpha, 20.2% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 265 through 268 No H-bonds generated for 'chain 'A' and resid 265 through 268' Processing helix chain 'A' and resid 318 through 333 removed outlier: 4.331A pdb=" N PHE A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 406 through 413 Processing helix chain 'A' and resid 452 through 459 Processing helix chain 'A' and resid 505 through 509 Processing helix chain 'A' and resid 511 through 521 Processing helix chain 'A' and resid 525 through 541 Processing helix chain 'A' and resid 543 through 552 removed outlier: 4.741A pdb=" N TRP A 552 " --> pdb=" O GLU A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 594 removed outlier: 4.010A pdb=" N THR A 593 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 589 through 594' Processing helix chain 'A' and resid 612 through 632 removed outlier: 5.289A pdb=" N ASP A 616 " --> pdb=" O ARG A 613 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N MET A 624 " --> pdb=" O LEU A 621 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 628 " --> pdb=" O LEU A 625 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N GLY A 630 " --> pdb=" O LYS A 627 " (cutoff:3.500A) Proline residue: A 631 - end of helix Processing helix chain 'A' and resid 649 through 662 Processing helix chain 'A' and resid 678 through 689 Processing helix chain 'A' and resid 701 through 705 Processing helix chain 'A' and resid 708 through 725 removed outlier: 4.452A pdb=" N ARG A 711 " --> pdb=" O THR A 708 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER A 712 " --> pdb=" O ARG A 709 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 713 " --> pdb=" O LEU A 710 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU A 725 " --> pdb=" O ASN A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 803 removed outlier: 3.972A pdb=" N LEU A 790 " --> pdb=" O ASP A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 827 removed outlier: 4.074A pdb=" N LYS A 823 " --> pdb=" O GLY A 820 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL A 825 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 826 " --> pdb=" O LYS A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 838 removed outlier: 3.819A pdb=" N LYS A 835 " --> pdb=" O PRO A 831 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N CYS A 836 " --> pdb=" O GLN A 832 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N PHE A 837 " --> pdb=" O LEU A 833 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLU A 838 " --> pdb=" O GLN A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 929 removed outlier: 3.639A pdb=" N CYS A 928 " --> pdb=" O THR A 924 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS A 929 " --> pdb=" O PHE A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 956 Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.963A pdb=" N GLU A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing sheet with id= A, first strand: chain 'A' and resid 562 through 567 Processing sheet with id= B, first strand: chain 'A' and resid 230 through 232 removed outlier: 3.586A pdb=" N LEU A 357 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 233 through 235 removed outlier: 3.541A pdb=" N ARG A 555 " --> pdb=" O GLN A 234 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 278 through 281 removed outlier: 3.592A pdb=" N LEU A 281 " --> pdb=" O TYR A 241 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL A 240 " --> pdb=" O LEU A 312 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 312 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 310 " --> pdb=" O GLN A 242 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N HIS A 244 " --> pdb=" O MET A 308 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N MET A 308 " --> pdb=" O HIS A 244 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N THR A 246 " --> pdb=" O ILE A 306 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N ILE A 306 " --> pdb=" O THR A 246 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 417 through 420 Processing sheet with id= F, first strand: chain 'A' and resid 431 through 433 removed outlier: 3.723A pdb=" N LEU A 471 " --> pdb=" O ASP A 433 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 491 " --> pdb=" O HIS A 474 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 572 through 574 Processing sheet with id= H, first strand: chain 'A' and resid 640 through 644 removed outlier: 3.566A pdb=" N ILE A 673 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 771 through 777 removed outlier: 3.955A pdb=" N SER A 763 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VAL A 741 " --> pdb=" O SER A 763 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS A 809 " --> pdb=" O MET A 740 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N ILE A 742 " --> pdb=" O LYS A 809 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N VAL A 811 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N MET A 744 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR A 813 " --> pdb=" O MET A 744 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N VAL A 746 " --> pdb=" O TYR A 813 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N LYS A 846 " --> pdb=" O ILE A 810 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL A 812 " --> pdb=" O LYS A 846 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL A 848 " --> pdb=" O VAL A 812 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N ARG A 814 " --> pdb=" O VAL A 848 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N PHE A 850 " --> pdb=" O ARG A 814 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 910 " --> pdb=" O VAL A 849 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL A 851 " --> pdb=" O CYS A 908 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N CYS A 908 " --> pdb=" O VAL A 851 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N GLN A 853 " --> pdb=" O TYR A 906 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N TYR A 906 " --> pdb=" O GLN A 853 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL A 887 " --> pdb=" O CYS A 908 " (cutoff:3.500A) 217 hydrogen bonds defined for protein. 552 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1465 1.33 - 1.45: 1327 1.45 - 1.57: 3595 1.57 - 1.69: 26 1.69 - 1.81: 74 Bond restraints: 6487 Sorted by residual: bond pdb=" C2 OMC B 26 " pdb=" N3 OMC B 26 " ideal model delta sigma weight residual 1.491 1.351 0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" N1 OMC B 26 " pdb=" C6 OMC B 26 " ideal model delta sigma weight residual 1.455 1.337 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C5 OMC B 26 " pdb=" C6 OMC B 26 " ideal model delta sigma weight residual 1.488 1.389 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" N3 OMC B 26 " pdb=" C4 OMC B 26 " ideal model delta sigma weight residual 1.448 1.351 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C4 OMC B 26 " pdb=" N4 OMC B 26 " ideal model delta sigma weight residual 1.452 1.355 0.097 2.00e-02 2.50e+03 2.37e+01 ... (remaining 6482 not shown) Histogram of bond angle deviations from ideal: 99.40 - 106.34: 287 106.34 - 113.28: 3531 113.28 - 120.21: 2340 120.21 - 127.15: 2579 127.15 - 134.09: 114 Bond angle restraints: 8851 Sorted by residual: angle pdb=" C4' U B 2 " pdb=" C3' U B 2 " pdb=" O3' U B 2 " ideal model delta sigma weight residual 113.00 122.15 -9.15 1.50e+00 4.44e-01 3.72e+01 angle pdb=" C3' OMC B 26 " pdb=" C2' OMC B 26 " pdb=" C1' OMC B 26 " ideal model delta sigma weight residual 101.50 105.78 -4.28 1.00e+00 1.00e+00 1.83e+01 angle pdb=" C3' U B 2 " pdb=" C2' U B 2 " pdb=" O2' U B 2 " ideal model delta sigma weight residual 110.70 104.81 5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" N THR A 880 " pdb=" CA THR A 880 " pdb=" CB THR A 880 " ideal model delta sigma weight residual 114.17 110.08 4.09 1.14e+00 7.69e-01 1.28e+01 angle pdb=" C3' U B 2 " pdb=" C2' U B 2 " pdb=" C1' U B 2 " ideal model delta sigma weight residual 101.30 104.79 -3.49 1.00e+00 1.00e+00 1.22e+01 ... (remaining 8846 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.74: 3412 18.74 - 37.47: 416 37.47 - 56.21: 82 56.21 - 74.95: 25 74.95 - 93.68: 8 Dihedral angle restraints: 3943 sinusoidal: 1757 harmonic: 2186 Sorted by residual: dihedral pdb=" CA SER A 248 " pdb=" C SER A 248 " pdb=" N PRO A 249 " pdb=" CA PRO A 249 " ideal model delta harmonic sigma weight residual 180.00 157.47 22.53 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ILE A 419 " pdb=" C ILE A 419 " pdb=" N THR A 420 " pdb=" CA THR A 420 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA TRP A 588 " pdb=" C TRP A 588 " pdb=" N VAL A 589 " pdb=" CA VAL A 589 " ideal model delta harmonic sigma weight residual -180.00 -159.92 -20.08 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 3940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 955 0.104 - 0.208: 50 0.208 - 0.311: 2 0.311 - 0.415: 0 0.415 - 0.519: 1 Chirality restraints: 1008 Sorted by residual: chirality pdb=" C3' U B 2 " pdb=" C4' U B 2 " pdb=" O3' U B 2 " pdb=" C2' U B 2 " both_signs ideal model delta sigma weight residual False -2.48 -1.96 -0.52 2.00e-01 2.50e+01 6.74e+00 chirality pdb=" P U B 2 " pdb=" OP1 U B 2 " pdb=" OP2 U B 2 " pdb=" O5' U B 2 " both_signs ideal model delta sigma weight residual True 2.41 -2.12 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CA ARG A 752 " pdb=" N ARG A 752 " pdb=" C ARG A 752 " pdb=" CB ARG A 752 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1005 not shown) Planarity restraints: 1069 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC B 26 " -0.501 2.00e-02 2.50e+03 4.07e-01 3.73e+03 pdb=" C4' OMC B 26 " 0.335 2.00e-02 2.50e+03 pdb=" O4' OMC B 26 " 0.614 2.00e-02 2.50e+03 pdb=" C3' OMC B 26 " -0.395 2.00e-02 2.50e+03 pdb=" O3' OMC B 26 " 0.342 2.00e-02 2.50e+03 pdb=" C2' OMC B 26 " -0.479 2.00e-02 2.50e+03 pdb=" O2' OMC B 26 " 0.017 2.00e-02 2.50e+03 pdb=" C1' OMC B 26 " 0.383 2.00e-02 2.50e+03 pdb=" N1 OMC B 26 " -0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 2 " 0.039 2.00e-02 2.50e+03 2.45e-02 1.36e+01 pdb=" N1 U B 2 " -0.030 2.00e-02 2.50e+03 pdb=" C2 U B 2 " -0.048 2.00e-02 2.50e+03 pdb=" O2 U B 2 " 0.016 2.00e-02 2.50e+03 pdb=" N3 U B 2 " 0.011 2.00e-02 2.50e+03 pdb=" C4 U B 2 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U B 2 " 0.016 2.00e-02 2.50e+03 pdb=" C5 U B 2 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U B 2 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 320 " 0.054 5.00e-02 4.00e+02 8.11e-02 1.05e+01 pdb=" N PRO A 321 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 321 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 321 " 0.045 5.00e-02 4.00e+02 ... (remaining 1066 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 65 2.56 - 3.14: 4916 3.14 - 3.73: 9423 3.73 - 4.31: 13280 4.31 - 4.90: 22167 Nonbonded interactions: 49851 Sorted by model distance: nonbonded pdb=" OP1 A B 3 " pdb="MG MG B1001 " model vdw 1.969 2.170 nonbonded pdb=" O LEU A 973 " pdb="MG MG B1001 " model vdw 1.974 2.170 nonbonded pdb=" OD2 ASP A 745 " pdb="MG MG A1001 " model vdw 2.111 2.170 nonbonded pdb=" NZ LYS A 949 " pdb=" OP1 C B 4 " model vdw 2.192 2.520 nonbonded pdb=" OH TYR A 422 " pdb=" OP1 OMC B 26 " model vdw 2.231 2.440 ... (remaining 49846 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: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.180 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 23.670 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 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 : 0.006 0.140 6487 Z= 0.353 Angle : 0.791 9.147 8851 Z= 0.436 Chirality : 0.050 0.519 1008 Planarity : 0.014 0.407 1069 Dihedral : 17.051 93.682 2527 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.45 % Allowed : 20.47 % Favored : 79.08 % 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: -0.16 (0.29), residues: 742 helix: 0.80 (0.32), residues: 240 sheet: -0.21 (0.37), residues: 179 loop : -0.62 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 552 HIS 0.003 0.001 HIS A 395 PHE 0.041 0.002 PHE A 580 TYR 0.034 0.002 TYR A 460 ARG 0.003 0.000 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 145 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.6699 (m-30) cc_final: 0.6162 (m-30) REVERT: A 317 ASP cc_start: 0.6378 (m-30) cc_final: 0.6115 (m-30) REVERT: A 402 LYS cc_start: 0.7798 (mttt) cc_final: 0.7492 (ptpt) REVERT: A 434 TRP cc_start: 0.7166 (m100) cc_final: 0.6944 (m100) REVERT: A 507 MET cc_start: 0.4827 (tmt) cc_final: 0.4317 (tmt) REVERT: A 617 GLN cc_start: 0.7234 (mp10) cc_final: 0.7018 (mp10) REVERT: A 674 MET cc_start: 0.7032 (tpp) cc_final: 0.6824 (tpp) outliers start: 3 outliers final: 2 residues processed: 147 average time/residue: 0.1973 time to fit residues: 37.6018 Evaluate side-chains 110 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 108 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 588 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 63 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 19 optimal weight: 8.9990 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 35 optimal weight: 0.0970 chunk 43 optimal weight: 5.9990 chunk 68 optimal weight: 6.9990 overall best weight: 2.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 561 HIS ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7018 moved from start: 0.2174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6487 Z= 0.341 Angle : 0.755 13.905 8851 Z= 0.420 Chirality : 0.047 0.154 1008 Planarity : 0.007 0.108 1069 Dihedral : 13.456 96.540 1023 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 5.19 % Allowed : 18.69 % Favored : 76.11 % 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: -0.34 (0.29), residues: 742 helix: 0.64 (0.32), residues: 235 sheet: -0.41 (0.36), residues: 191 loop : -0.64 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 588 HIS 0.007 0.001 HIS A 929 PHE 0.022 0.002 PHE A 322 TYR 0.023 0.002 TYR A 772 ARG 0.004 0.001 ARG A 295 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 107 time to evaluate : 0.704 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.6646 (m-30) cc_final: 0.6233 (m-30) REVERT: A 402 LYS cc_start: 0.7886 (mttt) cc_final: 0.7595 (ptpt) REVERT: A 507 MET cc_start: 0.5019 (tmt) cc_final: 0.4533 (tmt) outliers start: 35 outliers final: 23 residues processed: 131 average time/residue: 0.1785 time to fit residues: 31.1505 Evaluate side-chains 118 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 588 TRP Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 875 THR Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 970 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 37 optimal weight: 0.3980 chunk 21 optimal weight: 9.9990 chunk 56 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 0.0970 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN A 294 GLN A 722 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6487 Z= 0.166 Angle : 0.617 12.114 8851 Z= 0.353 Chirality : 0.042 0.141 1008 Planarity : 0.006 0.114 1069 Dihedral : 12.661 96.485 1023 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.41 % Allowed : 20.92 % Favored : 75.67 % 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: -0.10 (0.30), residues: 742 helix: 1.06 (0.34), residues: 227 sheet: -0.23 (0.37), residues: 185 loop : -0.68 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 606 HIS 0.003 0.000 HIS A 929 PHE 0.017 0.002 PHE A 322 TYR 0.012 0.001 TYR A 931 ARG 0.003 0.000 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: A 298 ASP cc_start: 0.6581 (m-30) cc_final: 0.6228 (m-30) REVERT: A 386 ARG cc_start: 0.6225 (tpp80) cc_final: 0.6020 (mmm-85) REVERT: A 436 LYS cc_start: 0.7874 (tptt) cc_final: 0.7607 (tptt) REVERT: A 507 MET cc_start: 0.5149 (tmt) cc_final: 0.4727 (tmt) REVERT: A 612 LYS cc_start: 0.8070 (tptp) cc_final: 0.7495 (tmmt) REVERT: A 860 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7445 (pp) REVERT: A 878 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6673 (p0) REVERT: A 884 CYS cc_start: 0.8095 (p) cc_final: 0.7852 (t) outliers start: 23 outliers final: 13 residues processed: 124 average time/residue: 0.1986 time to fit residues: 32.2010 Evaluate side-chains 116 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 722 ASN Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 970 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 67 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 68 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 60 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN A 355 HIS A 853 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.3152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6487 Z= 0.364 Angle : 0.719 12.047 8851 Z= 0.399 Chirality : 0.046 0.153 1008 Planarity : 0.007 0.113 1069 Dihedral : 12.569 98.748 1020 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 6.38 % Allowed : 19.44 % Favored : 74.18 % 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: -0.39 (0.30), residues: 742 helix: 0.82 (0.34), residues: 226 sheet: -0.41 (0.35), residues: 197 loop : -0.85 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 552 HIS 0.008 0.001 HIS A 929 PHE 0.021 0.003 PHE A 760 TYR 0.022 0.002 TYR A 772 ARG 0.005 0.001 ARG A 551 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 103 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 LYS cc_start: 0.7765 (tptt) cc_final: 0.7526 (tptt) REVERT: A 439 LYS cc_start: 0.8185 (tppt) cc_final: 0.7821 (pttt) REVERT: A 507 MET cc_start: 0.5162 (tmt) cc_final: 0.4850 (tmt) REVERT: A 551 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7006 (mtm-85) REVERT: A 860 LEU cc_start: 0.8098 (OUTLIER) cc_final: 0.7636 (pp) REVERT: A 884 CYS cc_start: 0.8244 (p) cc_final: 0.7805 (t) outliers start: 43 outliers final: 32 residues processed: 136 average time/residue: 0.1922 time to fit residues: 34.4966 Evaluate side-chains 130 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 97 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 255 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 432 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 559 ASP Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 909 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 37 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 722 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7001 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6487 Z= 0.200 Angle : 0.625 12.037 8851 Z= 0.356 Chirality : 0.042 0.138 1008 Planarity : 0.006 0.113 1069 Dihedral : 12.126 98.368 1020 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.90 % Allowed : 21.81 % Favored : 73.29 % 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: -0.23 (0.30), residues: 742 helix: 0.98 (0.35), residues: 226 sheet: -0.33 (0.38), residues: 180 loop : -0.76 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 932 HIS 0.005 0.001 HIS A 929 PHE 0.018 0.002 PHE A 322 TYR 0.013 0.001 TYR A 772 ARG 0.005 0.000 ARG A 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 106 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 436 LYS cc_start: 0.7795 (tptt) cc_final: 0.7558 (tptt) REVERT: A 439 LYS cc_start: 0.8006 (tppt) cc_final: 0.7690 (pttt) REVERT: A 444 MET cc_start: 0.7129 (mmm) cc_final: 0.6929 (mmm) REVERT: A 507 MET cc_start: 0.5267 (tmt) cc_final: 0.4944 (tmt) REVERT: A 551 ARG cc_start: 0.7817 (mtm-85) cc_final: 0.7191 (mtm-85) REVERT: A 665 LYS cc_start: 0.8426 (mmtt) cc_final: 0.7996 (mmmt) REVERT: A 860 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7612 (pp) REVERT: A 878 ASP cc_start: 0.7290 (OUTLIER) cc_final: 0.6762 (p0) REVERT: A 884 CYS cc_start: 0.8045 (p) cc_final: 0.7680 (t) outliers start: 33 outliers final: 24 residues processed: 129 average time/residue: 0.1970 time to fit residues: 32.9562 Evaluate side-chains 127 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 101 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 65 optimal weight: 4.9990 chunk 14 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 17 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6487 Z= 0.225 Angle : 0.639 12.059 8851 Z= 0.361 Chirality : 0.042 0.141 1008 Planarity : 0.006 0.113 1069 Dihedral : 12.047 101.298 1020 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.64 % Allowed : 22.40 % Favored : 71.96 % 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: -0.28 (0.30), residues: 742 helix: 1.01 (0.35), residues: 226 sheet: -0.39 (0.38), residues: 180 loop : -0.82 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 932 HIS 0.005 0.001 HIS A 929 PHE 0.017 0.002 PHE A 760 TYR 0.014 0.001 TYR A 772 ARG 0.008 0.001 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 101 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 439 LYS cc_start: 0.7957 (tppt) cc_final: 0.7733 (pttt) REVERT: A 507 MET cc_start: 0.5269 (tmt) cc_final: 0.4952 (tmt) REVERT: A 634 MET cc_start: 0.6983 (mmm) cc_final: 0.6665 (mmt) REVERT: A 860 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7615 (pp) REVERT: A 878 ASP cc_start: 0.7263 (OUTLIER) cc_final: 0.6732 (p0) REVERT: A 884 CYS cc_start: 0.8118 (p) cc_final: 0.7702 (t) outliers start: 38 outliers final: 32 residues processed: 128 average time/residue: 0.1912 time to fit residues: 32.2001 Evaluate side-chains 133 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 8 optimal weight: 0.9980 chunk 41 optimal weight: 0.1980 chunk 52 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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: 0.7070 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6487 Z= 0.316 Angle : 0.687 11.995 8851 Z= 0.384 Chirality : 0.044 0.148 1008 Planarity : 0.006 0.114 1069 Dihedral : 12.181 104.357 1020 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.79 % Allowed : 22.26 % Favored : 71.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.30), residues: 742 helix: 0.83 (0.35), residues: 227 sheet: -0.54 (0.38), residues: 179 loop : -0.96 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 932 HIS 0.006 0.001 HIS A 929 PHE 0.020 0.002 PHE A 760 TYR 0.019 0.002 TYR A 772 ARG 0.006 0.001 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 99 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 507 MET cc_start: 0.5278 (tmt) cc_final: 0.4977 (tmt) REVERT: A 551 ARG cc_start: 0.7952 (mtm-85) cc_final: 0.7750 (mtm-85) REVERT: A 860 LEU cc_start: 0.8154 (OUTLIER) cc_final: 0.7728 (pp) REVERT: A 878 ASP cc_start: 0.7267 (OUTLIER) cc_final: 0.6699 (p0) REVERT: A 884 CYS cc_start: 0.8154 (p) cc_final: 0.7719 (t) outliers start: 39 outliers final: 35 residues processed: 129 average time/residue: 0.1893 time to fit residues: 32.2252 Evaluate side-chains 132 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 95 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 647 ASP Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 721 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6487 Z= 0.184 Angle : 0.627 12.028 8851 Z= 0.355 Chirality : 0.042 0.135 1008 Planarity : 0.006 0.113 1069 Dihedral : 11.904 103.776 1020 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.79 % Allowed : 23.15 % Favored : 71.07 % 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: -0.41 (0.30), residues: 742 helix: 0.98 (0.35), residues: 226 sheet: -0.47 (0.38), residues: 180 loop : -0.96 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 932 HIS 0.004 0.001 HIS A 929 PHE 0.018 0.002 PHE A 952 TYR 0.014 0.001 TYR A 243 ARG 0.006 0.001 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 104 time to evaluate : 0.642 Fit side-chains revert: symmetry clash REVERT: A 507 MET cc_start: 0.5348 (OUTLIER) cc_final: 0.5003 (tmt) REVERT: A 665 LYS cc_start: 0.8339 (mmtt) cc_final: 0.7914 (mmmt) REVERT: A 860 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7637 (pp) REVERT: A 878 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6738 (p0) REVERT: A 884 CYS cc_start: 0.8133 (p) cc_final: 0.7696 (t) outliers start: 39 outliers final: 31 residues processed: 131 average time/residue: 0.1834 time to fit residues: 31.7054 Evaluate side-chains 133 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 99 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 940 VAL Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 63 optimal weight: 0.0980 chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.6991 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6487 Z= 0.184 Angle : 0.623 11.986 8851 Z= 0.354 Chirality : 0.042 0.135 1008 Planarity : 0.006 0.113 1069 Dihedral : 11.794 102.597 1020 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 5.79 % Allowed : 24.18 % Favored : 70.03 % 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: -0.38 (0.30), residues: 742 helix: 1.02 (0.35), residues: 225 sheet: -0.44 (0.37), residues: 189 loop : -0.97 (0.32), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 932 HIS 0.003 0.001 HIS A 929 PHE 0.019 0.002 PHE A 952 TYR 0.015 0.002 TYR A 243 ARG 0.007 0.001 ARG A 329 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 104 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 386 ARG cc_start: 0.6079 (tpp80) cc_final: 0.5792 (mmm-85) REVERT: A 402 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7514 (ptpt) REVERT: A 507 MET cc_start: 0.5203 (OUTLIER) cc_final: 0.4954 (tmt) REVERT: A 551 ARG cc_start: 0.7844 (mtm-85) cc_final: 0.7618 (mtm-85) REVERT: A 665 LYS cc_start: 0.8360 (mmtt) cc_final: 0.7920 (mmmt) REVERT: A 860 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7660 (pp) REVERT: A 878 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6751 (p0) REVERT: A 884 CYS cc_start: 0.8145 (p) cc_final: 0.7712 (t) outliers start: 39 outliers final: 34 residues processed: 131 average time/residue: 0.2023 time to fit residues: 35.0560 Evaluate side-chains 138 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 100 time to evaluate : 0.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 854 LYS Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 33 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 68 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 overall best weight: 1.4782 ------------------------------------------------------------------------------- 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: 0.7021 moved from start: 0.4092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6487 Z= 0.235 Angle : 0.650 11.998 8851 Z= 0.366 Chirality : 0.042 0.148 1008 Planarity : 0.006 0.113 1069 Dihedral : 11.835 103.128 1020 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 5.64 % Allowed : 24.33 % Favored : 70.03 % 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: -0.39 (0.30), residues: 742 helix: 1.01 (0.35), residues: 225 sheet: -0.45 (0.38), residues: 179 loop : -0.96 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 932 HIS 0.004 0.001 HIS A 929 PHE 0.019 0.002 PHE A 952 TYR 0.016 0.002 TYR A 243 ARG 0.005 0.001 ARG A 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 103 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 386 ARG cc_start: 0.6116 (tpp80) cc_final: 0.5792 (mmm-85) REVERT: A 402 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7633 (ptpt) REVERT: A 507 MET cc_start: 0.5120 (OUTLIER) cc_final: 0.4862 (tmt) REVERT: A 665 LYS cc_start: 0.8391 (mmtt) cc_final: 0.7938 (mmmt) REVERT: A 860 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7735 (pp) REVERT: A 878 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6826 (p0) REVERT: A 884 CYS cc_start: 0.8201 (p) cc_final: 0.7792 (t) outliers start: 38 outliers final: 32 residues processed: 129 average time/residue: 0.1912 time to fit residues: 32.9598 Evaluate side-chains 135 residues out of total 674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 99 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 248 SER Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 342 ASN Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 412 LEU Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 582 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 624 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 671 CYS Chi-restraints excluded: chain A residue 672 ILE Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain A residue 796 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 857 SER Chi-restraints excluded: chain A residue 860 LEU Chi-restraints excluded: chain A residue 861 TYR Chi-restraints excluded: chain A residue 862 LEU Chi-restraints excluded: chain A residue 866 GLN Chi-restraints excluded: chain A residue 878 ASP Chi-restraints excluded: chain A residue 883 SER Chi-restraints excluded: chain A residue 888 ASP Chi-restraints excluded: chain A residue 891 LEU Chi-restraints excluded: chain A residue 953 LEU Chi-restraints excluded: chain A residue 964 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 54 optimal weight: 2.9990 chunk 8 optimal weight: 20.0000 chunk 16 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.0770 chunk 52 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 43 optimal weight: 6.9990 overall best weight: 1.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.188269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.147158 restraints weight = 8431.222| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 2.58 r_work: 0.3718 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6487 Z= 0.232 Angle : 0.654 12.005 8851 Z= 0.367 Chirality : 0.043 0.148 1008 Planarity : 0.006 0.114 1069 Dihedral : 11.827 103.493 1020 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.49 % Allowed : 24.18 % Favored : 70.33 % 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: -0.37 (0.30), residues: 742 helix: 1.01 (0.35), residues: 224 sheet: -0.39 (0.39), residues: 179 loop : -0.96 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 932 HIS 0.004 0.001 HIS A 929 PHE 0.019 0.002 PHE A 952 TYR 0.015 0.002 TYR A 243 ARG 0.006 0.000 ARG A 329 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1694.79 seconds wall clock time: 31 minutes 38.19 seconds (1898.19 seconds total)