Starting phenix.real_space_refine on Fri Jul 19 06:45:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/07_2024/8sxt_40858_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/07_2024/8sxt_40858.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/07_2024/8sxt_40858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/07_2024/8sxt_40858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/07_2024/8sxt_40858_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/07_2024/8sxt_40858_neut.cif" } resolution = 3.3 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= 0.032 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 20 5.49 5 Mg 1 5.21 5 S 20 5.16 5 C 4061 2.51 5 N 1080 2.21 5 O 1200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 406": "OE1" <-> "OE2" Residue "A GLU 413": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A TYR 481": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 700": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A PHE 847": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 994": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1056": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 6382 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 225 Classifications: {'RNA': 11} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna2p': 1, 'rna3p': 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' U%5*END:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "A" Number of atoms: 5987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5987 Classifications: {'peptide': 726} Link IDs: {'PTRANS': 33, 'TRANS': 692} Chain breaks: 1 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'TTP': 1} Classifications: {'undetermined': 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} Time building chain proxies: 4.51, per 1000 atoms: 0.71 Number of scatterers: 6382 At special positions: 0 Unit cell: (92.02, 87.72, 110.94, 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 20 16.00 P 20 15.00 Mg 1 11.99 O 1200 8.00 N 1080 7.00 C 4061 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: 2.85 Conformation dependent library (CDL) restraints added in 1.0 seconds 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 4 sheets defined 64.0% alpha, 5.1% beta 5 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 2.18 Creating SS restraints... Processing helix chain 'A' and resid 255 through 258 Processing helix chain 'A' and resid 259 through 275 Processing helix chain 'A' and resid 283 through 310 Processing helix chain 'A' and resid 403 through 419 removed outlier: 3.644A pdb=" N GLN A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 removed outlier: 3.685A pdb=" N ASP A 430 " --> pdb=" O LEU A 426 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE A 432 " --> pdb=" O GLU A 428 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 435 " --> pdb=" O THR A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 450 Processing helix chain 'A' and resid 455 through 463 removed outlier: 3.749A pdb=" N VAL A 459 " --> pdb=" O GLY A 455 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 460 " --> pdb=" O SER A 456 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 484 removed outlier: 3.687A pdb=" N TYR A 481 " --> pdb=" O THR A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 503 removed outlier: 3.625A pdb=" N LEU A 488 " --> pdb=" O TYR A 484 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Proline residue: A 490 - end of helix removed outlier: 4.233A pdb=" N LYS A 494 " --> pdb=" O PRO A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 removed outlier: 3.768A pdb=" N TYR A 510 " --> pdb=" O ASN A 507 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU A 511 " --> pdb=" O SER A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 528 No H-bonds generated for 'chain 'A' and resid 526 through 528' Processing helix chain 'A' and resid 537 through 559 removed outlier: 4.445A pdb=" N HIS A 554 " --> pdb=" O ARG A 550 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 5.949A pdb=" N LYS A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 589 removed outlier: 3.889A pdb=" N ILE A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS A 578 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 608 removed outlier: 3.990A pdb=" N ILE A 608 " --> pdb=" O PHE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 620 Processing helix chain 'A' and resid 624 through 634 removed outlier: 3.619A pdb=" N ALA A 632 " --> pdb=" O LYS A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.624A pdb=" N VAL A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU A 675 " --> pdb=" O VAL A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 710 through 730 removed outlier: 4.483A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 757 removed outlier: 3.741A pdb=" N GLU A 750 " --> pdb=" O ASN A 746 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER A 751 " --> pdb=" O ARG A 747 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN A 752 " --> pdb=" O GLN A 748 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE A 753 " --> pdb=" O THR A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 778 No H-bonds generated for 'chain 'A' and resid 776 through 778' Processing helix chain 'A' and resid 779 through 785 Processing helix chain 'A' and resid 785 through 799 removed outlier: 3.711A pdb=" N ASN A 797 " --> pdb=" O LYS A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 817 Processing helix chain 'A' and resid 817 through 828 Processing helix chain 'A' and resid 833 through 850 removed outlier: 4.042A pdb=" N PHE A 837 " --> pdb=" O PRO A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 863 Processing helix chain 'A' and resid 864 through 868 Processing helix chain 'A' and resid 874 through 885 Processing helix chain 'A' and resid 885 through 893 removed outlier: 4.249A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 898 through 902 Processing helix chain 'A' and resid 911 through 915 removed outlier: 3.646A pdb=" N LEU A 915 " --> pdb=" O TYR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 947 Processing helix chain 'A' and resid 961 through 966 removed outlier: 3.870A pdb=" N LYS A 965 " --> pdb=" O SER A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 981 removed outlier: 4.126A pdb=" N ILE A 974 " --> pdb=" O LYS A 970 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 975 " --> pdb=" O PRO A 971 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR A 976 " --> pdb=" O LYS A 972 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU A 977 " --> pdb=" O THR A 973 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 989 removed outlier: 4.033A pdb=" N ILE A 988 " --> pdb=" O THR A 984 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY A 989 " --> pdb=" O ILE A 985 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 984 through 989' Processing helix chain 'A' and resid 990 through 994 removed outlier: 3.923A pdb=" N PHE A 994 " --> pdb=" O GLY A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1005 Processing helix chain 'A' and resid 1006 through 1008 No H-bonds generated for 'chain 'A' and resid 1006 through 1008' Processing helix chain 'A' and resid 1009 through 1022 removed outlier: 3.733A pdb=" N LYS A1015 " --> pdb=" O TRP A1011 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA A1022 " --> pdb=" O SER A1018 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1030 Processing helix chain 'A' and resid 1034 through 1041 removed outlier: 3.575A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1048 through 1061 Processing sheet with id=AA1, first strand: chain 'A' and resid 530 through 535 removed outlier: 6.050A pdb=" N ILE A 514 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 697 through 698 removed outlier: 3.506A pdb=" N MET A 704 " --> pdb=" O ILE A 599 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLN A 739 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 740 " --> pdb=" O THR A 760 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690 Processing sheet with id=AA4, first strand: chain 'A' and resid 767 through 768 285 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 13 hydrogen bonds 26 hydrogen bond angles 0 basepair planarities 5 basepair parallelities 7 stacking parallelities Total time for adding SS restraints: 1.85 Time building geometry restraints manager: 3.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1001 1.32 - 1.44: 1772 1.44 - 1.57: 3710 1.57 - 1.69: 38 1.69 - 1.82: 34 Bond restraints: 6555 Sorted by residual: bond pdb=" C PRO A 518 " pdb=" O PRO A 518 " ideal model delta sigma weight residual 1.233 1.197 0.036 1.23e-02 6.61e+03 8.78e+00 bond pdb=" C ILE A 517 " pdb=" N PRO A 518 " ideal model delta sigma weight residual 1.331 1.357 -0.026 1.20e-02 6.94e+03 4.71e+00 bond pdb=" CA LYS A 519 " pdb=" C LYS A 519 " ideal model delta sigma weight residual 1.523 1.504 0.018 1.28e-02 6.10e+03 2.08e+00 bond pdb=" CA LYS A 519 " pdb=" CB LYS A 519 " ideal model delta sigma weight residual 1.526 1.511 0.016 1.36e-02 5.41e+03 1.30e+00 bond pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 1.468 1.455 0.013 1.20e-02 6.94e+03 1.15e+00 ... (remaining 6550 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.49: 252 106.49 - 113.75: 3731 113.75 - 121.00: 3188 121.00 - 128.26: 1694 128.26 - 135.51: 67 Bond angle restraints: 8932 Sorted by residual: angle pdb=" C ILE A 517 " pdb=" N PRO A 518 " pdb=" CA PRO A 518 " ideal model delta sigma weight residual 119.83 135.51 -15.68 1.08e+00 8.57e-01 2.11e+02 angle pdb=" CB MET A 625 " pdb=" CG MET A 625 " pdb=" SD MET A 625 " ideal model delta sigma weight residual 112.70 125.03 -12.33 3.00e+00 1.11e-01 1.69e+01 angle pdb=" O ILE A 517 " pdb=" C ILE A 517 " pdb=" N PRO A 518 " ideal model delta sigma weight residual 121.10 125.42 -4.32 1.14e+00 7.69e-01 1.43e+01 angle pdb=" N PRO A 518 " pdb=" CA PRO A 518 " pdb=" C PRO A 518 " ideal model delta sigma weight residual 111.03 105.99 5.04 1.54e+00 4.22e-01 1.07e+01 angle pdb=" C LEU A 488 " pdb=" N VAL A 489 " pdb=" CA VAL A 489 " ideal model delta sigma weight residual 120.33 122.72 -2.39 8.00e-01 1.56e+00 8.94e+00 ... (remaining 8927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.59: 3729 29.59 - 59.17: 241 59.17 - 88.76: 19 88.76 - 118.34: 2 118.34 - 147.93: 1 Dihedral angle restraints: 3992 sinusoidal: 1844 harmonic: 2148 Sorted by residual: dihedral pdb=" C2 TTP C 101 " pdb=" C1' TTP C 101 " pdb=" N1 TTP C 101 " pdb=" O4' TTP C 101 " ideal model delta sinusoidal sigma weight residual 301.68 153.76 147.93 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" O5' TTP C 101 " pdb=" O3A TTP C 101 " pdb=" PA TTP C 101 " pdb=" PB TTP C 101 " ideal model delta sinusoidal sigma weight residual 180.02 95.33 84.69 1 2.00e+01 2.50e-03 2.18e+01 dihedral pdb=" CB GLU A 310 " pdb=" CG GLU A 310 " pdb=" CD GLU A 310 " pdb=" OE1 GLU A 310 " ideal model delta sinusoidal sigma weight residual 0.00 -89.01 89.01 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 3989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 584 0.025 - 0.051: 253 0.051 - 0.076: 100 0.076 - 0.102: 45 0.102 - 0.127: 17 Chirality restraints: 999 Sorted by residual: chirality pdb=" CA ILE A 596 " pdb=" N ILE A 596 " pdb=" C ILE A 596 " pdb=" CB ILE A 596 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.04e-01 chirality pdb=" CA SER A 664 " pdb=" N SER A 664 " pdb=" C SER A 664 " pdb=" CB SER A 664 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA PRO A 490 " pdb=" N PRO A 490 " pdb=" C PRO A 490 " pdb=" CB PRO A 490 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 996 not shown) Planarity restraints: 1050 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 908 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 909 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 909 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 909 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 813 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C VAL A 813 " 0.028 2.00e-02 2.50e+03 pdb=" O VAL A 813 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS A 814 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 799 " -0.011 2.00e-02 2.50e+03 9.11e-03 2.08e+00 pdb=" CG TRP A 799 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 799 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 799 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 799 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 799 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 799 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 799 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 799 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP A 799 " 0.002 2.00e-02 2.50e+03 ... (remaining 1047 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 80 2.61 - 3.18: 5443 3.18 - 3.76: 10039 3.76 - 4.33: 12997 4.33 - 4.90: 21343 Nonbonded interactions: 49902 Sorted by model distance: nonbonded pdb=" O ALA A 601 " pdb="MG MG A1301 " model vdw 2.039 2.170 nonbonded pdb=" O SER A 508 " pdb=" ND2 ASN A 537 " model vdw 2.293 2.520 nonbonded pdb=" O GLN A 748 " pdb=" NE2 GLN A 752 " model vdw 2.299 2.520 nonbonded pdb=" O ALA A 540 " pdb=" ND2 ASN A 544 " model vdw 2.303 2.520 nonbonded pdb=" ND2 ASN A 442 " pdb=" OE2 GLU A 445 " model vdw 2.313 2.520 ... (remaining 49897 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 23.040 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 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 0.050 6555 Z= 0.167 Angle : 0.600 15.684 8932 Z= 0.342 Chirality : 0.038 0.127 999 Planarity : 0.003 0.043 1050 Dihedral : 17.793 147.928 2596 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 0.45 % Allowed : 27.90 % Favored : 71.64 % 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: 0.31 (0.32), residues: 722 helix: 1.09 (0.28), residues: 376 sheet: -0.83 (0.83), residues: 42 loop : -0.70 (0.37), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 799 HIS 0.004 0.001 HIS A 263 PHE 0.012 0.001 PHE A 496 TYR 0.007 0.001 TYR A 484 ARG 0.004 0.000 ARG A 809 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 211 time to evaluate : 0.728 Fit side-chains REVERT: A 286 ASN cc_start: 0.7995 (m110) cc_final: 0.7751 (p0) REVERT: A 422 LYS cc_start: 0.8418 (tttt) cc_final: 0.7825 (ttmt) REVERT: A 457 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7413 (mt-10) REVERT: A 458 ILE cc_start: 0.8548 (mt) cc_final: 0.8271 (tt) REVERT: A 468 LYS cc_start: 0.8648 (mmmm) cc_final: 0.8396 (mmmm) REVERT: A 494 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7975 (mtpt) REVERT: A 495 LEU cc_start: 0.8785 (tp) cc_final: 0.8567 (tt) REVERT: A 502 GLU cc_start: 0.7289 (tp30) cc_final: 0.6727 (tp30) REVERT: A 555 ILE cc_start: 0.8016 (tp) cc_final: 0.7690 (tp) REVERT: A 618 ASN cc_start: 0.8222 (t0) cc_final: 0.7921 (t0) REVERT: A 631 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7646 (ttp80) REVERT: A 677 ARG cc_start: 0.8115 (mtt90) cc_final: 0.7694 (mtt-85) REVERT: A 681 GLN cc_start: 0.7897 (mm110) cc_final: 0.7615 (mm110) REVERT: A 686 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7811 (ttmm) REVERT: A 704 MET cc_start: 0.7541 (ttp) cc_final: 0.7294 (ttp) REVERT: A 720 LYS cc_start: 0.7933 (ptmm) cc_final: 0.7629 (ptpp) REVERT: A 761 ILE cc_start: 0.8318 (mp) cc_final: 0.7605 (mp) REVERT: A 810 ILE cc_start: 0.8947 (mt) cc_final: 0.8650 (tt) REVERT: A 841 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7235 (mm-30) REVERT: A 844 THR cc_start: 0.8486 (m) cc_final: 0.8275 (m) REVERT: A 958 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7842 (mtpp) REVERT: A 969 VAL cc_start: 0.8041 (m) cc_final: 0.7812 (t) REVERT: A 1002 MET cc_start: 0.7375 (mmt) cc_final: 0.7050 (mmt) REVERT: A 1011 TRP cc_start: 0.6936 (m100) cc_final: 0.6714 (m100) REVERT: A 1024 GLU cc_start: 0.8076 (pm20) cc_final: 0.7835 (pm20) outliers start: 3 outliers final: 2 residues processed: 213 average time/residue: 0.2544 time to fit residues: 66.4128 Evaluate side-chains 187 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 272 MET Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.0770 chunk 58 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 67 optimal weight: 0.0270 overall best weight: 0.3774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 ASN A 581 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 851 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6555 Z= 0.173 Angle : 0.554 6.512 8932 Z= 0.284 Chirality : 0.040 0.144 999 Planarity : 0.004 0.039 1050 Dihedral : 11.299 147.842 1027 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 4.83 % Allowed : 25.49 % Favored : 69.68 % 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 (0.32), residues: 722 helix: 1.27 (0.27), residues: 384 sheet: -0.66 (0.83), residues: 42 loop : -0.72 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 799 HIS 0.010 0.002 HIS A 560 PHE 0.020 0.002 PHE A 668 TYR 0.012 0.001 TYR A 415 ARG 0.003 0.000 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 197 time to evaluate : 0.698 Fit side-chains REVERT: A 272 MET cc_start: 0.7747 (ptm) cc_final: 0.7380 (ptm) REVERT: A 422 LYS cc_start: 0.8380 (tttt) cc_final: 0.7878 (ttmt) REVERT: A 428 GLU cc_start: 0.7090 (tt0) cc_final: 0.6609 (tt0) REVERT: A 435 THR cc_start: 0.8475 (p) cc_final: 0.8130 (t) REVERT: A 444 GLU cc_start: 0.7544 (mp0) cc_final: 0.7271 (mp0) REVERT: A 457 GLU cc_start: 0.7753 (mt-10) cc_final: 0.7472 (mt-10) REVERT: A 458 ILE cc_start: 0.8510 (mt) cc_final: 0.8255 (tt) REVERT: A 468 LYS cc_start: 0.8695 (mmmm) cc_final: 0.8397 (mtpp) REVERT: A 469 LYS cc_start: 0.8277 (mmmt) cc_final: 0.8041 (mmmm) REVERT: A 482 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.6400 (tp-100) REVERT: A 485 LYS cc_start: 0.8496 (tttp) cc_final: 0.8137 (tptm) REVERT: A 486 GLU cc_start: 0.8378 (pt0) cc_final: 0.8013 (pt0) REVERT: A 494 LYS cc_start: 0.8291 (mtmt) cc_final: 0.7950 (ptpt) REVERT: A 502 GLU cc_start: 0.7305 (tp30) cc_final: 0.6732 (tp30) REVERT: A 606 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7152 (m-30) REVERT: A 614 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7973 (mt) REVERT: A 618 ASN cc_start: 0.8214 (t0) cc_final: 0.7889 (t0) REVERT: A 619 LYS cc_start: 0.8704 (tptp) cc_final: 0.8155 (tttp) REVERT: A 625 MET cc_start: 0.6729 (tmm) cc_final: 0.6500 (tmm) REVERT: A 631 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7762 (ttp80) REVERT: A 677 ARG cc_start: 0.8096 (mtt90) cc_final: 0.7784 (mtt-85) REVERT: A 681 GLN cc_start: 0.7958 (mm110) cc_final: 0.7635 (mm110) REVERT: A 686 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7937 (ttmm) REVERT: A 720 LYS cc_start: 0.8040 (ptmm) cc_final: 0.7710 (ptpp) REVERT: A 735 VAL cc_start: 0.5084 (p) cc_final: 0.4411 (m) REVERT: A 761 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7869 (mp) REVERT: A 765 ARG cc_start: 0.7741 (OUTLIER) cc_final: 0.7163 (mtm-85) REVERT: A 783 GLU cc_start: 0.7404 (tp30) cc_final: 0.7122 (tp30) REVERT: A 807 VAL cc_start: 0.8493 (m) cc_final: 0.8249 (p) REVERT: A 810 ILE cc_start: 0.8931 (mt) cc_final: 0.8636 (tt) REVERT: A 841 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7325 (mm-30) REVERT: A 936 CYS cc_start: 0.8090 (t) cc_final: 0.7844 (t) REVERT: A 1002 MET cc_start: 0.7324 (mmt) cc_final: 0.6937 (mmt) REVERT: A 1011 TRP cc_start: 0.6979 (m100) cc_final: 0.6701 (m100) REVERT: A 1050 ILE cc_start: 0.8636 (mm) cc_final: 0.8398 (mt) REVERT: A 1056 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7460 (mm-30) outliers start: 32 outliers final: 14 residues processed: 217 average time/residue: 0.2337 time to fit residues: 63.4299 Evaluate side-chains 206 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 55 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6555 Z= 0.201 Angle : 0.553 8.355 8932 Z= 0.287 Chirality : 0.041 0.139 999 Planarity : 0.003 0.035 1050 Dihedral : 11.265 148.419 1024 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.88 % Favored : 95.98 % Rotamer: Outliers : 4.37 % Allowed : 26.24 % Favored : 69.38 % 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: 0.61 (0.32), residues: 722 helix: 1.55 (0.27), residues: 384 sheet: -1.02 (0.80), residues: 44 loop : -0.89 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 937 HIS 0.005 0.001 HIS A 560 PHE 0.012 0.001 PHE A 847 TYR 0.009 0.001 TYR A 415 ARG 0.003 0.000 ARG A 483 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7741 (ptm) cc_final: 0.7341 (ptm) REVERT: A 422 LYS cc_start: 0.8295 (tttt) cc_final: 0.7936 (ttmt) REVERT: A 428 GLU cc_start: 0.7133 (tt0) cc_final: 0.6682 (tt0) REVERT: A 444 GLU cc_start: 0.7594 (mp0) cc_final: 0.7330 (mp0) REVERT: A 458 ILE cc_start: 0.8529 (mt) cc_final: 0.8269 (tt) REVERT: A 468 LYS cc_start: 0.8763 (mmmm) cc_final: 0.8459 (mmmm) REVERT: A 482 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.6525 (tp-100) REVERT: A 485 LYS cc_start: 0.8544 (tttp) cc_final: 0.8241 (tptm) REVERT: A 486 GLU cc_start: 0.8374 (pt0) cc_final: 0.7988 (pt0) REVERT: A 502 GLU cc_start: 0.7399 (tp30) cc_final: 0.6848 (tp30) REVERT: A 591 ASP cc_start: 0.8060 (t0) cc_final: 0.7754 (t0) REVERT: A 602 GLU cc_start: 0.7247 (tt0) cc_final: 0.6959 (tt0) REVERT: A 618 ASN cc_start: 0.8341 (t0) cc_final: 0.8052 (t0) REVERT: A 619 LYS cc_start: 0.8872 (tptp) cc_final: 0.8617 (tptm) REVERT: A 631 ARG cc_start: 0.8064 (ttm-80) cc_final: 0.7793 (ttp80) REVERT: A 677 ARG cc_start: 0.8241 (mtt90) cc_final: 0.7829 (mtt-85) REVERT: A 681 GLN cc_start: 0.8099 (mm110) cc_final: 0.7776 (mm110) REVERT: A 686 LYS cc_start: 0.8440 (ttmt) cc_final: 0.8150 (ttmm) REVERT: A 707 TYR cc_start: 0.8684 (OUTLIER) cc_final: 0.8344 (m-80) REVERT: A 735 VAL cc_start: 0.5223 (p) cc_final: 0.4579 (m) REVERT: A 741 PHE cc_start: 0.8396 (m-10) cc_final: 0.8196 (m-10) REVERT: A 754 MET cc_start: 0.7496 (tpt) cc_final: 0.7011 (tpt) REVERT: A 761 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 765 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7203 (mtm-85) REVERT: A 776 ASP cc_start: 0.7793 (t0) cc_final: 0.7399 (t0) REVERT: A 783 GLU cc_start: 0.7597 (tp30) cc_final: 0.7336 (tp30) REVERT: A 810 ILE cc_start: 0.8966 (mt) cc_final: 0.8660 (tt) REVERT: A 812 ILE cc_start: 0.8166 (mm) cc_final: 0.7940 (mm) REVERT: A 841 GLU cc_start: 0.7626 (mm-30) cc_final: 0.7330 (mm-30) REVERT: A 846 LYS cc_start: 0.8623 (mttm) cc_final: 0.7983 (mttm) REVERT: A 883 VAL cc_start: 0.8473 (t) cc_final: 0.8060 (t) REVERT: A 922 LYS cc_start: 0.7826 (mmmt) cc_final: 0.7616 (mmmt) REVERT: A 936 CYS cc_start: 0.8096 (t) cc_final: 0.7784 (t) REVERT: A 953 LEU cc_start: 0.8039 (tp) cc_final: 0.7726 (tp) REVERT: A 1002 MET cc_start: 0.7307 (mmt) cc_final: 0.6927 (mmt) REVERT: A 1011 TRP cc_start: 0.7063 (m100) cc_final: 0.6806 (m100) REVERT: A 1050 ILE cc_start: 0.8650 (mm) cc_final: 0.8429 (mt) outliers start: 29 outliers final: 16 residues processed: 209 average time/residue: 0.2424 time to fit residues: 62.5175 Evaluate side-chains 209 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 189 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 708 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 5.9990 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6555 Z= 0.217 Angle : 0.564 8.387 8932 Z= 0.288 Chirality : 0.042 0.167 999 Planarity : 0.004 0.034 1050 Dihedral : 11.105 148.858 1024 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 4.68 % Allowed : 27.15 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.33), residues: 722 helix: 1.61 (0.28), residues: 385 sheet: -1.06 (0.80), residues: 44 loop : -0.81 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 940 HIS 0.007 0.001 HIS A 263 PHE 0.010 0.001 PHE A 847 TYR 0.012 0.001 TYR A 484 ARG 0.005 0.000 ARG A 945 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 203 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7711 (ptm) cc_final: 0.7318 (ptm) REVERT: A 422 LYS cc_start: 0.8279 (tttt) cc_final: 0.7972 (ttmt) REVERT: A 428 GLU cc_start: 0.7123 (tt0) cc_final: 0.6675 (tt0) REVERT: A 444 GLU cc_start: 0.7625 (mp0) cc_final: 0.7369 (mp0) REVERT: A 468 LYS cc_start: 0.8783 (mmmm) cc_final: 0.8414 (mmmm) REVERT: A 483 ARG cc_start: 0.7916 (tmm-80) cc_final: 0.7543 (tmm-80) REVERT: A 485 LYS cc_start: 0.8542 (tttp) cc_final: 0.8235 (tptm) REVERT: A 486 GLU cc_start: 0.8372 (pt0) cc_final: 0.8074 (pt0) REVERT: A 502 GLU cc_start: 0.7389 (tp30) cc_final: 0.6852 (tp30) REVERT: A 510 TYR cc_start: 0.8084 (m-80) cc_final: 0.7724 (m-80) REVERT: A 570 MET cc_start: 0.8410 (mmm) cc_final: 0.7601 (mmm) REVERT: A 591 ASP cc_start: 0.8159 (t0) cc_final: 0.7860 (t0) REVERT: A 593 ASN cc_start: 0.8142 (t0) cc_final: 0.7754 (t0) REVERT: A 602 GLU cc_start: 0.7296 (tt0) cc_final: 0.6943 (tt0) REVERT: A 618 ASN cc_start: 0.8408 (t0) cc_final: 0.8158 (t0) REVERT: A 677 ARG cc_start: 0.8345 (mtt90) cc_final: 0.7876 (mtt-85) REVERT: A 681 GLN cc_start: 0.8209 (mm110) cc_final: 0.7851 (mm110) REVERT: A 686 LYS cc_start: 0.8443 (ttmt) cc_final: 0.8171 (ttmm) REVERT: A 707 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8197 (m-80) REVERT: A 735 VAL cc_start: 0.5518 (p) cc_final: 0.4907 (m) REVERT: A 741 PHE cc_start: 0.8349 (m-10) cc_final: 0.8124 (m-10) REVERT: A 754 MET cc_start: 0.7543 (tpt) cc_final: 0.7151 (tpt) REVERT: A 761 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8092 (mp) REVERT: A 776 ASP cc_start: 0.7885 (t0) cc_final: 0.7500 (t0) REVERT: A 810 ILE cc_start: 0.8950 (mt) cc_final: 0.8659 (tt) REVERT: A 812 ILE cc_start: 0.8391 (mm) cc_final: 0.8085 (mm) REVERT: A 836 PHE cc_start: 0.8358 (t80) cc_final: 0.8011 (t80) REVERT: A 910 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6592 (p90) REVERT: A 929 ASP cc_start: 0.6293 (OUTLIER) cc_final: 0.5883 (m-30) REVERT: A 953 LEU cc_start: 0.7852 (tp) cc_final: 0.7507 (tp) REVERT: A 984 THR cc_start: 0.7830 (p) cc_final: 0.7503 (t) REVERT: A 1002 MET cc_start: 0.7394 (mmt) cc_final: 0.6983 (mmt) REVERT: A 1011 TRP cc_start: 0.7142 (m100) cc_final: 0.6864 (m100) REVERT: A 1050 ILE cc_start: 0.8633 (mm) cc_final: 0.8421 (mt) outliers start: 31 outliers final: 21 residues processed: 221 average time/residue: 0.2274 time to fit residues: 62.7249 Evaluate side-chains 222 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 0.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 983 ILE Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 36 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6555 Z= 0.222 Angle : 0.560 8.066 8932 Z= 0.289 Chirality : 0.042 0.146 999 Planarity : 0.004 0.032 1050 Dihedral : 11.050 149.489 1024 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 5.43 % Allowed : 27.60 % Favored : 66.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.66 (0.32), residues: 722 helix: 1.58 (0.27), residues: 391 sheet: -1.03 (0.81), residues: 44 loop : -0.90 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 940 HIS 0.004 0.001 HIS A 263 PHE 0.010 0.001 PHE A 725 TYR 0.008 0.001 TYR A 415 ARG 0.004 0.000 ARG A 945 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 201 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7725 (ptm) cc_final: 0.7297 (ptm) REVERT: A 422 LYS cc_start: 0.8281 (tttt) cc_final: 0.7951 (ttmt) REVERT: A 428 GLU cc_start: 0.7132 (tt0) cc_final: 0.6653 (tt0) REVERT: A 444 GLU cc_start: 0.7649 (mp0) cc_final: 0.7398 (mp0) REVERT: A 468 LYS cc_start: 0.8812 (mmmm) cc_final: 0.8399 (mmmm) REVERT: A 482 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.6706 (tp40) REVERT: A 483 ARG cc_start: 0.7861 (tmm-80) cc_final: 0.7418 (tmm-80) REVERT: A 485 LYS cc_start: 0.8509 (tttp) cc_final: 0.8236 (tptm) REVERT: A 486 GLU cc_start: 0.8326 (pt0) cc_final: 0.7783 (pt0) REVERT: A 497 GLN cc_start: 0.8081 (mt0) cc_final: 0.7869 (mt0) REVERT: A 502 GLU cc_start: 0.7377 (tp30) cc_final: 0.7065 (tp30) REVERT: A 510 TYR cc_start: 0.8108 (m-80) cc_final: 0.7841 (m-80) REVERT: A 570 MET cc_start: 0.8415 (mmm) cc_final: 0.7642 (mmm) REVERT: A 591 ASP cc_start: 0.8211 (t0) cc_final: 0.7943 (t0) REVERT: A 593 ASN cc_start: 0.8178 (t0) cc_final: 0.7704 (t0) REVERT: A 602 GLU cc_start: 0.7289 (tt0) cc_final: 0.6950 (tt0) REVERT: A 618 ASN cc_start: 0.8447 (t0) cc_final: 0.8226 (t0) REVERT: A 677 ARG cc_start: 0.8376 (mtt90) cc_final: 0.7892 (mtt-85) REVERT: A 681 GLN cc_start: 0.8236 (mm110) cc_final: 0.7865 (mm110) REVERT: A 707 TYR cc_start: 0.8660 (OUTLIER) cc_final: 0.7979 (m-80) REVERT: A 735 VAL cc_start: 0.5769 (p) cc_final: 0.5240 (m) REVERT: A 765 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7381 (mtm-85) REVERT: A 776 ASP cc_start: 0.7924 (t0) cc_final: 0.7555 (t0) REVERT: A 791 GLU cc_start: 0.7858 (tm-30) cc_final: 0.7291 (tm-30) REVERT: A 802 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.6976 (mp) REVERT: A 810 ILE cc_start: 0.8899 (mt) cc_final: 0.8635 (tt) REVERT: A 812 ILE cc_start: 0.8509 (mm) cc_final: 0.8187 (mm) REVERT: A 836 PHE cc_start: 0.8379 (t80) cc_final: 0.8032 (t80) REVERT: A 910 HIS cc_start: 0.6947 (OUTLIER) cc_final: 0.6595 (p90) REVERT: A 929 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.5843 (m-30) REVERT: A 953 LEU cc_start: 0.7832 (tp) cc_final: 0.7512 (tp) REVERT: A 962 ARG cc_start: 0.8325 (ttp80) cc_final: 0.7998 (ttp80) REVERT: A 969 VAL cc_start: 0.8337 (m) cc_final: 0.8133 (t) REVERT: A 1002 MET cc_start: 0.7361 (mmt) cc_final: 0.6970 (mmt) REVERT: A 1011 TRP cc_start: 0.7212 (m100) cc_final: 0.6940 (m100) REVERT: A 1050 ILE cc_start: 0.8650 (mm) cc_final: 0.8447 (mt) outliers start: 36 outliers final: 20 residues processed: 222 average time/residue: 0.2266 time to fit residues: 62.9757 Evaluate side-chains 218 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 192 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 284 TYR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 995 MET Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 646 GLN ** A 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 6555 Z= 0.237 Angle : 0.587 8.240 8932 Z= 0.304 Chirality : 0.043 0.146 999 Planarity : 0.004 0.032 1050 Dihedral : 11.027 150.499 1024 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.02 % Favored : 95.84 % Rotamer: Outliers : 5.28 % Allowed : 30.47 % Favored : 64.25 % 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: 0.61 (0.32), residues: 722 helix: 1.50 (0.27), residues: 391 sheet: -1.12 (0.79), residues: 44 loop : -0.86 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 940 HIS 0.005 0.001 HIS A 263 PHE 0.014 0.002 PHE A 781 TYR 0.008 0.001 TYR A1061 ARG 0.008 0.000 ARG A 945 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 201 time to evaluate : 0.720 Fit side-chains REVERT: A 272 MET cc_start: 0.7712 (ptm) cc_final: 0.7294 (ptm) REVERT: A 428 GLU cc_start: 0.7128 (tt0) cc_final: 0.6627 (tt0) REVERT: A 444 GLU cc_start: 0.7674 (mp0) cc_final: 0.7421 (mp0) REVERT: A 468 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8425 (mmmm) REVERT: A 485 LYS cc_start: 0.8510 (tttp) cc_final: 0.8240 (tptm) REVERT: A 486 GLU cc_start: 0.8341 (pt0) cc_final: 0.8095 (pt0) REVERT: A 497 GLN cc_start: 0.8135 (mt0) cc_final: 0.7929 (mt0) REVERT: A 502 GLU cc_start: 0.7390 (tp30) cc_final: 0.7154 (tp30) REVERT: A 591 ASP cc_start: 0.8225 (t0) cc_final: 0.7974 (t0) REVERT: A 593 ASN cc_start: 0.8175 (t0) cc_final: 0.7740 (t0) REVERT: A 602 GLU cc_start: 0.7315 (tt0) cc_final: 0.6932 (tt0) REVERT: A 631 ARG cc_start: 0.8189 (ttp80) cc_final: 0.7877 (ttm170) REVERT: A 636 LYS cc_start: 0.8409 (ptpp) cc_final: 0.8156 (ptpp) REVERT: A 677 ARG cc_start: 0.8412 (mtt90) cc_final: 0.8155 (mtt-85) REVERT: A 710 ASN cc_start: 0.7654 (m-40) cc_final: 0.7439 (m-40) REVERT: A 735 VAL cc_start: 0.5820 (p) cc_final: 0.5307 (m) REVERT: A 776 ASP cc_start: 0.7936 (t0) cc_final: 0.7543 (t0) REVERT: A 783 GLU cc_start: 0.7795 (tp30) cc_final: 0.7382 (tp30) REVERT: A 810 ILE cc_start: 0.8868 (mt) cc_final: 0.8612 (tt) REVERT: A 812 ILE cc_start: 0.8546 (mm) cc_final: 0.8232 (mm) REVERT: A 836 PHE cc_start: 0.8404 (t80) cc_final: 0.8049 (t80) REVERT: A 910 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6596 (p90) REVERT: A 929 ASP cc_start: 0.6233 (OUTLIER) cc_final: 0.5982 (m-30) REVERT: A 953 LEU cc_start: 0.7765 (tp) cc_final: 0.7469 (tp) REVERT: A 962 ARG cc_start: 0.8360 (ttp80) cc_final: 0.7971 (ttp80) REVERT: A 967 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7784 (pp) REVERT: A 969 VAL cc_start: 0.8471 (m) cc_final: 0.8239 (t) REVERT: A 984 THR cc_start: 0.8013 (m) cc_final: 0.7489 (t) REVERT: A 1002 MET cc_start: 0.7414 (mmt) cc_final: 0.6985 (mmt) REVERT: A 1011 TRP cc_start: 0.7225 (m100) cc_final: 0.6959 (m100) REVERT: A 1050 ILE cc_start: 0.8673 (mm) cc_final: 0.8466 (mt) outliers start: 35 outliers final: 22 residues processed: 221 average time/residue: 0.2240 time to fit residues: 61.7187 Evaluate side-chains 218 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 844 THR Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain A residue 929 ASP Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1021 THR Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.0970 chunk 8 optimal weight: 9.9990 chunk 40 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 60 optimal weight: 0.0170 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 28 optimal weight: 0.9980 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6555 Z= 0.161 Angle : 0.557 8.067 8932 Z= 0.286 Chirality : 0.041 0.152 999 Planarity : 0.004 0.031 1050 Dihedral : 10.944 150.464 1024 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.46 % Favored : 96.40 % Rotamer: Outliers : 3.47 % Allowed : 32.88 % Favored : 63.65 % 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 (0.32), residues: 722 helix: 1.56 (0.27), residues: 383 sheet: -1.02 (0.82), residues: 44 loop : -0.70 (0.37), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 940 HIS 0.004 0.001 HIS A 263 PHE 0.015 0.001 PHE A 781 TYR 0.009 0.001 TYR A 415 ARG 0.007 0.000 ARG A 945 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 195 time to evaluate : 0.700 Fit side-chains REVERT: A 428 GLU cc_start: 0.7085 (tt0) cc_final: 0.6547 (tt0) REVERT: A 444 GLU cc_start: 0.7637 (mp0) cc_final: 0.7376 (mp0) REVERT: A 468 LYS cc_start: 0.8832 (mmmm) cc_final: 0.8387 (mmmm) REVERT: A 485 LYS cc_start: 0.8463 (tttp) cc_final: 0.8165 (tptt) REVERT: A 486 GLU cc_start: 0.8328 (pt0) cc_final: 0.8107 (pt0) REVERT: A 502 GLU cc_start: 0.7338 (tp30) cc_final: 0.7113 (tp30) REVERT: A 591 ASP cc_start: 0.8192 (t0) cc_final: 0.7945 (t0) REVERT: A 593 ASN cc_start: 0.8147 (t0) cc_final: 0.7699 (t0) REVERT: A 602 GLU cc_start: 0.7261 (tt0) cc_final: 0.6910 (tt0) REVERT: A 677 ARG cc_start: 0.8390 (mtt90) cc_final: 0.8110 (mtt-85) REVERT: A 735 VAL cc_start: 0.5523 (p) cc_final: 0.5054 (m) REVERT: A 776 ASP cc_start: 0.7907 (t0) cc_final: 0.7507 (t0) REVERT: A 791 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7357 (tm-30) REVERT: A 810 ILE cc_start: 0.8864 (mt) cc_final: 0.8626 (tt) REVERT: A 812 ILE cc_start: 0.8520 (mm) cc_final: 0.8192 (mm) REVERT: A 836 PHE cc_start: 0.8385 (t80) cc_final: 0.8056 (t80) REVERT: A 846 LYS cc_start: 0.8586 (mttm) cc_final: 0.7929 (mttm) REVERT: A 910 HIS cc_start: 0.6911 (OUTLIER) cc_final: 0.6574 (p90) REVERT: A 914 TYR cc_start: 0.7427 (m-10) cc_final: 0.7158 (m-80) REVERT: A 962 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7928 (ttp80) REVERT: A 969 VAL cc_start: 0.8458 (m) cc_final: 0.8249 (t) REVERT: A 984 THR cc_start: 0.8016 (m) cc_final: 0.7491 (t) REVERT: A 1002 MET cc_start: 0.7381 (mmt) cc_final: 0.6908 (mmt) REVERT: A 1011 TRP cc_start: 0.7188 (m100) cc_final: 0.6925 (m100) REVERT: A 1050 ILE cc_start: 0.8648 (mm) cc_final: 0.8434 (mt) REVERT: A 1052 ARG cc_start: 0.8826 (mtp180) cc_final: 0.8618 (mtm180) outliers start: 23 outliers final: 19 residues processed: 210 average time/residue: 0.2322 time to fit residues: 60.5991 Evaluate side-chains 209 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 189 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1021 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 0.0020 chunk 35 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.4525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6555 Z= 0.197 Angle : 0.574 10.434 8932 Z= 0.292 Chirality : 0.042 0.157 999 Planarity : 0.004 0.032 1050 Dihedral : 10.937 150.968 1024 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 4.37 % Allowed : 32.43 % Favored : 63.20 % 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 (0.32), residues: 722 helix: 1.57 (0.27), residues: 392 sheet: -1.07 (0.81), residues: 44 loop : -0.78 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 899 HIS 0.004 0.001 HIS A 263 PHE 0.015 0.001 PHE A 781 TYR 0.007 0.001 TYR A 415 ARG 0.006 0.000 ARG A 945 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 187 time to evaluate : 0.699 Fit side-chains REVERT: A 275 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.6008 (mp0) REVERT: A 428 GLU cc_start: 0.7140 (tt0) cc_final: 0.6578 (tt0) REVERT: A 444 GLU cc_start: 0.7671 (mp0) cc_final: 0.7408 (mp0) REVERT: A 468 LYS cc_start: 0.8840 (mmmm) cc_final: 0.8387 (mmmm) REVERT: A 485 LYS cc_start: 0.8462 (tttp) cc_final: 0.8184 (tptt) REVERT: A 486 GLU cc_start: 0.8332 (pt0) cc_final: 0.8117 (pt0) REVERT: A 591 ASP cc_start: 0.8202 (t0) cc_final: 0.7959 (t0) REVERT: A 602 GLU cc_start: 0.7293 (tt0) cc_final: 0.6924 (tt0) REVERT: A 677 ARG cc_start: 0.8432 (mtt90) cc_final: 0.8161 (mtt-85) REVERT: A 735 VAL cc_start: 0.5691 (p) cc_final: 0.5253 (m) REVERT: A 765 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7298 (mtm-85) REVERT: A 776 ASP cc_start: 0.7958 (t0) cc_final: 0.7554 (t0) REVERT: A 783 GLU cc_start: 0.7851 (tp30) cc_final: 0.7461 (tp30) REVERT: A 810 ILE cc_start: 0.8854 (mt) cc_final: 0.8615 (tt) REVERT: A 812 ILE cc_start: 0.8545 (mm) cc_final: 0.8220 (mm) REVERT: A 836 PHE cc_start: 0.8407 (t80) cc_final: 0.8041 (t80) REVERT: A 846 LYS cc_start: 0.8601 (mttm) cc_final: 0.7917 (mttm) REVERT: A 910 HIS cc_start: 0.6920 (OUTLIER) cc_final: 0.6615 (p90) REVERT: A 953 LEU cc_start: 0.7647 (tp) cc_final: 0.7351 (tp) REVERT: A 962 ARG cc_start: 0.8367 (ttp80) cc_final: 0.8002 (ttp80) REVERT: A 969 VAL cc_start: 0.8503 (m) cc_final: 0.8276 (t) REVERT: A 984 THR cc_start: 0.7963 (m) cc_final: 0.7421 (t) REVERT: A 1002 MET cc_start: 0.7388 (mmt) cc_final: 0.6919 (mmt) REVERT: A 1011 TRP cc_start: 0.7215 (m100) cc_final: 0.6931 (m100) REVERT: A 1050 ILE cc_start: 0.8672 (mm) cc_final: 0.8460 (mt) REVERT: A 1052 ARG cc_start: 0.8850 (mtp180) cc_final: 0.8627 (mtm180) outliers start: 29 outliers final: 21 residues processed: 208 average time/residue: 0.2350 time to fit residues: 60.8721 Evaluate side-chains 208 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 184 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1021 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 0.1980 chunk 40 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 70 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6555 Z= 0.186 Angle : 0.587 8.522 8932 Z= 0.294 Chirality : 0.041 0.162 999 Planarity : 0.004 0.032 1050 Dihedral : 10.886 151.158 1024 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.16 % Favored : 95.71 % Rotamer: Outliers : 3.77 % Allowed : 33.18 % Favored : 63.05 % 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: 0.73 (0.32), residues: 722 helix: 1.56 (0.27), residues: 390 sheet: -1.08 (0.82), residues: 44 loop : -0.73 (0.37), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 940 HIS 0.003 0.001 HIS A 263 PHE 0.025 0.002 PHE A1019 TYR 0.007 0.001 TYR A 415 ARG 0.006 0.000 ARG A 945 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 185 time to evaluate : 0.718 Fit side-chains REVERT: A 412 ARG cc_start: 0.8267 (mtp180) cc_final: 0.7719 (mtp180) REVERT: A 428 GLU cc_start: 0.7125 (tt0) cc_final: 0.6577 (tt0) REVERT: A 444 GLU cc_start: 0.7640 (mp0) cc_final: 0.7401 (mp0) REVERT: A 468 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8383 (mmmm) REVERT: A 485 LYS cc_start: 0.8403 (tttp) cc_final: 0.8170 (tptt) REVERT: A 591 ASP cc_start: 0.8196 (t0) cc_final: 0.7956 (t0) REVERT: A 602 GLU cc_start: 0.7291 (tt0) cc_final: 0.6914 (tt0) REVERT: A 635 ASP cc_start: 0.7832 (t70) cc_final: 0.7326 (t0) REVERT: A 677 ARG cc_start: 0.8418 (mtt90) cc_final: 0.8142 (mtt-85) REVERT: A 735 VAL cc_start: 0.5717 (p) cc_final: 0.5289 (m) REVERT: A 783 GLU cc_start: 0.7836 (tp30) cc_final: 0.7605 (tp30) REVERT: A 812 ILE cc_start: 0.8545 (mm) cc_final: 0.8217 (mm) REVERT: A 834 MET cc_start: 0.7794 (mmm) cc_final: 0.7202 (tmm) REVERT: A 836 PHE cc_start: 0.8401 (t80) cc_final: 0.8054 (t80) REVERT: A 846 LYS cc_start: 0.8597 (mttm) cc_final: 0.7921 (mttm) REVERT: A 910 HIS cc_start: 0.6934 (OUTLIER) cc_final: 0.6649 (p90) REVERT: A 958 LYS cc_start: 0.8457 (mttm) cc_final: 0.8152 (mttp) REVERT: A 984 THR cc_start: 0.7971 (m) cc_final: 0.7442 (t) REVERT: A 1002 MET cc_start: 0.7426 (mmt) cc_final: 0.6998 (mmt) REVERT: A 1011 TRP cc_start: 0.7225 (m100) cc_final: 0.6928 (m100) REVERT: A 1050 ILE cc_start: 0.8660 (mm) cc_final: 0.8447 (mt) REVERT: A 1052 ARG cc_start: 0.8844 (mtp180) cc_final: 0.8637 (mtm180) outliers start: 25 outliers final: 21 residues processed: 200 average time/residue: 0.2514 time to fit residues: 61.8985 Evaluate side-chains 203 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 181 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1021 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.0570 chunk 48 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6555 Z= 0.185 Angle : 0.599 8.636 8932 Z= 0.303 Chirality : 0.042 0.175 999 Planarity : 0.004 0.033 1050 Dihedral : 10.893 151.284 1024 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.02 % Favored : 95.84 % Rotamer: Outliers : 3.92 % Allowed : 33.63 % Favored : 62.44 % 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 (0.32), residues: 722 helix: 1.58 (0.27), residues: 392 sheet: -1.14 (0.81), residues: 44 loop : -0.75 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 899 HIS 0.002 0.000 HIS A 263 PHE 0.022 0.002 PHE A1019 TYR 0.007 0.001 TYR A 415 ARG 0.006 0.000 ARG A 945 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1444 Ramachandran restraints generated. 722 Oldfield, 0 Emsley, 722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 191 time to evaluate : 0.759 Fit side-chains REVERT: A 428 GLU cc_start: 0.7138 (tt0) cc_final: 0.6604 (tt0) REVERT: A 468 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8377 (mmmm) REVERT: A 485 LYS cc_start: 0.8395 (tttp) cc_final: 0.8181 (tptt) REVERT: A 591 ASP cc_start: 0.8194 (t0) cc_final: 0.7960 (t0) REVERT: A 602 GLU cc_start: 0.7285 (tt0) cc_final: 0.6924 (tt0) REVERT: A 677 ARG cc_start: 0.8427 (mtt90) cc_final: 0.8140 (mtt-85) REVERT: A 735 VAL cc_start: 0.5743 (p) cc_final: 0.5348 (m) REVERT: A 783 GLU cc_start: 0.7813 (tp30) cc_final: 0.7583 (tp30) REVERT: A 812 ILE cc_start: 0.8545 (mm) cc_final: 0.8221 (mm) REVERT: A 834 MET cc_start: 0.7794 (mmm) cc_final: 0.7190 (tmm) REVERT: A 836 PHE cc_start: 0.8408 (t80) cc_final: 0.8064 (t80) REVERT: A 846 LYS cc_start: 0.8589 (mttm) cc_final: 0.7925 (mttm) REVERT: A 910 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6650 (p90) REVERT: A 958 LYS cc_start: 0.8434 (mttm) cc_final: 0.8136 (mttp) REVERT: A 984 THR cc_start: 0.7940 (m) cc_final: 0.7408 (t) REVERT: A 1002 MET cc_start: 0.7446 (mmt) cc_final: 0.7030 (mmt) REVERT: A 1011 TRP cc_start: 0.7218 (m100) cc_final: 0.6924 (m100) REVERT: A 1050 ILE cc_start: 0.8674 (mm) cc_final: 0.8458 (mt) REVERT: A 1052 ARG cc_start: 0.8847 (mtp180) cc_final: 0.8637 (mtm180) outliers start: 26 outliers final: 23 residues processed: 206 average time/residue: 0.2426 time to fit residues: 61.8270 Evaluate side-chains 207 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 183 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 443 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 590 LYS Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 754 MET Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 807 VAL Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 913 ASN Chi-restraints excluded: chain A residue 963 TRP Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1021 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 50.0000 chunk 8 optimal weight: 0.0570 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 chunk 24 optimal weight: 0.6980 chunk 60 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 594 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN A 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.139735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116979 restraints weight = 10543.337| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.81 r_work: 0.3351 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6555 Z= 0.179 Angle : 0.601 8.696 8932 Z= 0.302 Chirality : 0.041 0.174 999 Planarity : 0.004 0.030 1050 Dihedral : 10.845 151.285 1024 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.02 % Favored : 95.84 % Rotamer: Outliers : 3.92 % Allowed : 33.63 % Favored : 62.44 % 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: 0.68 (0.32), residues: 722 helix: 1.54 (0.27), residues: 389 sheet: -1.30 (0.80), residues: 44 loop : -0.73 (0.37), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 940 HIS 0.003 0.001 HIS A 554 PHE 0.022 0.002 PHE A1019 TYR 0.008 0.001 TYR A 284 ARG 0.006 0.000 ARG A 945 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2025.63 seconds wall clock time: 37 minutes 39.64 seconds (2259.64 seconds total)