Starting phenix.real_space_refine on Fri Apr 5 23:49:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/04_2024/8sxt_40858_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/04_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_40858/04_2024/8sxt_40858.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/04_2024/8sxt_40858.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/04_2024/8sxt_40858_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxt_40858/04_2024/8sxt_40858_updated.pdb" } 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: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 4.55, 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: 2.69 Conformation dependent library (CDL) restraints added in 984.9 milliseconds 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... running ksdssp... Secondary structure from input PDB file: 39 helices and 3 sheets defined 54.1% alpha, 4.7% beta 5 base pairs and 7 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 260 through 274 Processing helix chain 'A' and resid 284 through 309 Processing helix chain 'A' and resid 404 through 418 removed outlier: 3.644A pdb=" N GLN A 408 " --> pdb=" O PRO A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 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 443 through 449 Processing helix chain 'A' and resid 456 through 462 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 478 through 483 Processing helix chain 'A' and resid 485 through 502 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 507 through 510 removed outlier: 3.768A pdb=" N TYR A 510 " --> pdb=" O ASN A 507 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 507 through 510' Processing helix chain 'A' and resid 527 through 529 No H-bonds generated for 'chain 'A' and resid 527 through 529' Processing helix chain 'A' and resid 538 through 558 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 588 removed outlier: 4.269A pdb=" N ARG A 577 " --> pdb=" O PHE A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 607 No H-bonds generated for 'chain 'A' and resid 605 through 607' Processing helix chain 'A' and resid 610 through 619 Processing helix chain 'A' and resid 625 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 664 through 681 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 711 through 729 removed outlier: 4.483A pdb=" N GLN A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 756 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 777 through 784 removed outlier: 4.677A pdb=" N PHE A 781 " --> pdb=" O LYS A 778 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN A 784 " --> pdb=" O PHE A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 798 removed outlier: 3.711A pdb=" N ASN A 797 " --> pdb=" O LYS A 793 " (cutoff:3.500A) Processing helix chain 'A' and resid 806 through 816 Processing helix chain 'A' and resid 818 through 827 Processing helix chain 'A' and resid 834 through 849 Processing helix chain 'A' and resid 858 through 862 Processing helix chain 'A' and resid 865 through 867 No H-bonds generated for 'chain 'A' and resid 865 through 867' Processing helix chain 'A' and resid 875 through 892 removed outlier: 4.542A pdb=" N THR A 886 " --> pdb=" O THR A 882 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N ALA A 887 " --> pdb=" O VAL A 883 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N TRP A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N TYR A 889 " --> pdb=" O LYS A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 901 No H-bonds generated for 'chain 'A' and resid 899 through 901' Processing helix chain 'A' and resid 912 through 914 No H-bonds generated for 'chain 'A' and resid 912 through 914' Processing helix chain 'A' and resid 934 through 946 Processing helix chain 'A' and resid 962 through 965 No H-bonds generated for 'chain 'A' and resid 962 through 965' Processing helix chain 'A' and resid 971 through 980 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 985 through 988 No H-bonds generated for 'chain 'A' and resid 985 through 988' Processing helix chain 'A' and resid 991 through 993 No H-bonds generated for 'chain 'A' and resid 991 through 993' Processing helix chain 'A' and resid 999 through 1007 removed outlier: 4.672A pdb=" N ASP A1006 " --> pdb=" O MET A1002 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYS A1007 " --> pdb=" O ALA A1003 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1021 removed outlier: 3.733A pdb=" N LYS A1015 " --> pdb=" O TRP A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1023 through 1029 Processing helix chain 'A' and resid 1035 through 1041 removed outlier: 3.575A pdb=" N PHE A1040 " --> pdb=" O TRP A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1060 Processing sheet with id= A, first strand: chain 'A' and resid 530 through 535 removed outlier: 6.762A pdb=" N ASN A 640 " --> pdb=" O ILE A 514 " (cutoff:3.500A) removed outlier: 8.677A pdb=" N LEU A 516 " --> pdb=" O ASN A 640 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N ILE A 642 " --> pdb=" O LEU A 516 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 739 through 744 removed outlier: 3.899A pdb=" N GLN A 739 " --> pdb=" O SER A 598 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N MET A 704 " --> pdb=" O ILE A 599 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 765 through 768 removed outlier: 3.616A pdb=" N ILE A 766 " --> pdb=" O LEU A 773 " (cutoff:3.500A) 228 hydrogen bonds defined for protein. 630 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: 1.82 Time building geometry restraints manager: 2.88 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: 82 2.61 - 3.18: 5485 3.18 - 3.76: 10081 3.76 - 4.33: 13117 4.33 - 4.90: 21365 Nonbonded interactions: 50130 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 50125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 3.440 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 22.670 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.070 ------------------------------------------------------------------------------- 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= 0.168 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 : 0.674 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: 0.2524 time to fit residues: 66.0094 Evaluate side-chains 187 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 185 time to evaluate : 0.747 ------------------------------------------------------------------------------- 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: 0.8980 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 263 HIS ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6555 Z= 0.214 Angle : 0.572 7.070 8932 Z= 0.291 Chirality : 0.041 0.153 999 Planarity : 0.004 0.037 1050 Dihedral : 11.343 148.915 1027 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.32 % Favored : 96.54 % Rotamer: Outliers : 5.58 % Allowed : 24.74 % 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: 0.19 (0.32), residues: 722 helix: 1.00 (0.27), residues: 384 sheet: -0.65 (0.85), residues: 42 loop : -0.86 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 799 HIS 0.011 0.002 HIS A 560 PHE 0.020 0.002 PHE A 668 TYR 0.010 0.001 TYR A 415 ARG 0.005 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 234 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 197 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7752 (ptm) cc_final: 0.7366 (ptm) REVERT: A 286 ASN cc_start: 0.7999 (m110) cc_final: 0.7753 (p0) REVERT: A 422 LYS cc_start: 0.8336 (tttt) cc_final: 0.7882 (ttmt) REVERT: A 424 GLU cc_start: 0.7843 (pm20) cc_final: 0.7632 (pm20) REVERT: A 444 GLU cc_start: 0.7670 (mp0) cc_final: 0.7432 (mp0) REVERT: A 458 ILE cc_start: 0.8605 (mt) cc_final: 0.8290 (tt) REVERT: A 468 LYS cc_start: 0.8764 (mmmm) cc_final: 0.8458 (mmmm) REVERT: A 469 LYS cc_start: 0.8399 (mmmt) cc_final: 0.8183 (mmmm) REVERT: A 482 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.6526 (tp-100) REVERT: A 485 LYS cc_start: 0.8596 (tttp) cc_final: 0.8194 (tptm) REVERT: A 486 GLU cc_start: 0.8367 (pt0) cc_final: 0.7960 (pt0) REVERT: A 502 GLU cc_start: 0.7332 (tp30) cc_final: 0.6757 (tp30) REVERT: A 505 LEU cc_start: 0.8513 (mp) cc_final: 0.8171 (mp) REVERT: A 516 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.5227 (mt) REVERT: A 555 ILE cc_start: 0.8196 (tp) cc_final: 0.7864 (tp) REVERT: A 570 MET cc_start: 0.8393 (mmm) cc_final: 0.7603 (mmm) REVERT: A 591 ASP cc_start: 0.8135 (t0) cc_final: 0.7812 (t0) REVERT: A 602 GLU cc_start: 0.7222 (tt0) cc_final: 0.6995 (tt0) REVERT: A 618 ASN cc_start: 0.8300 (t0) cc_final: 0.7973 (t0) REVERT: A 619 LYS cc_start: 0.8682 (tptp) cc_final: 0.8434 (tptm) REVERT: A 625 MET cc_start: 0.6650 (tmm) cc_final: 0.6446 (tmm) REVERT: A 631 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7865 (ttp80) REVERT: A 677 ARG cc_start: 0.8249 (mtt90) cc_final: 0.7805 (mtt-85) REVERT: A 681 GLN cc_start: 0.8027 (mm110) cc_final: 0.7714 (mm110) REVERT: A 686 LYS cc_start: 0.8352 (ttmt) cc_final: 0.8078 (ttmm) REVERT: A 707 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8517 (m-80) REVERT: A 720 LYS cc_start: 0.8151 (ptmm) cc_final: 0.7821 (ptpp) REVERT: A 735 VAL cc_start: 0.5284 (p) cc_final: 0.4594 (m) REVERT: A 761 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8184 (mt) REVERT: A 764 LYS cc_start: 0.7891 (mmmt) cc_final: 0.7627 (mmmm) REVERT: A 765 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7332 (mtm-85) REVERT: A 791 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7293 (tm-30) REVERT: A 810 ILE cc_start: 0.8923 (OUTLIER) cc_final: 0.8605 (tt) REVERT: A 841 GLU cc_start: 0.7622 (mm-30) cc_final: 0.7357 (mm-30) REVERT: A 846 LYS cc_start: 0.8540 (mttm) cc_final: 0.7898 (mttm) REVERT: A 936 CYS cc_start: 0.8138 (t) cc_final: 0.7878 (t) REVERT: A 937 TRP cc_start: 0.8591 (t-100) cc_final: 0.8209 (t-100) REVERT: A 958 LYS cc_start: 0.8365 (mtpt) cc_final: 0.8116 (mttm) REVERT: A 964 ILE cc_start: 0.8149 (pt) cc_final: 0.7902 (pt) REVERT: A 1002 MET cc_start: 0.7366 (mmt) cc_final: 0.7035 (mmt) REVERT: A 1011 TRP cc_start: 0.6992 (m100) cc_final: 0.6737 (m100) REVERT: A 1018 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8694 (p) REVERT: A 1024 GLU cc_start: 0.8103 (pm20) cc_final: 0.7877 (pm20) REVERT: A 1050 ILE cc_start: 0.8672 (mm) cc_final: 0.8457 (mt) REVERT: A 1056 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7413 (mm-30) outliers start: 37 outliers final: 15 residues processed: 217 average time/residue: 0.2436 time to fit residues: 66.0069 Evaluate side-chains 208 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 ASN Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 614 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 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 848 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 Chi-restraints excluded: chain A residue 1018 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.0670 chunk 20 optimal weight: 0.0370 chunk 55 optimal weight: 0.0870 chunk 45 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 67 optimal weight: 3.9990 chunk 72 optimal weight: 0.0050 chunk 59 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 54 optimal weight: 0.0270 overall best weight: 0.0446 ------------------------------------------------------------------------------- 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 851 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6555 Z= 0.133 Angle : 0.512 8.585 8932 Z= 0.262 Chirality : 0.039 0.137 999 Planarity : 0.003 0.036 1050 Dihedral : 11.185 148.392 1024 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.05 % Favored : 96.81 % Rotamer: Outliers : 4.22 % Allowed : 26.55 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.32), residues: 722 helix: 1.17 (0.27), residues: 381 sheet: -0.61 (0.84), residues: 44 loop : -0.71 (0.37), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 940 HIS 0.004 0.001 HIS A 560 PHE 0.009 0.001 PHE A 847 TYR 0.012 0.001 TYR A 743 ARG 0.004 0.000 ARG A 945 *********************** 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 222 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 194 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: A 272 MET cc_start: 0.7730 (ptm) cc_final: 0.7317 (ptm) REVERT: A 286 ASN cc_start: 0.8006 (m110) cc_final: 0.7757 (p0) REVERT: A 422 LYS cc_start: 0.8347 (tttt) cc_final: 0.7839 (ttmt) REVERT: A 424 GLU cc_start: 0.7822 (pm20) cc_final: 0.7486 (pm20) REVERT: A 444 GLU cc_start: 0.7615 (mp0) cc_final: 0.7392 (mp0) REVERT: A 457 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7630 (mt-10) REVERT: A 458 ILE cc_start: 0.8596 (mt) cc_final: 0.8273 (tt) REVERT: A 468 LYS cc_start: 0.8720 (mmmm) cc_final: 0.8426 (mmmm) REVERT: A 482 GLN cc_start: 0.7566 (mt0) cc_final: 0.6608 (tp-100) REVERT: A 485 LYS cc_start: 0.8559 (tttp) cc_final: 0.8175 (tptm) REVERT: A 486 GLU cc_start: 0.8369 (pt0) cc_final: 0.8104 (pt0) REVERT: A 502 GLU cc_start: 0.7316 (tp30) cc_final: 0.6791 (tp30) REVERT: A 505 LEU cc_start: 0.8550 (mp) cc_final: 0.8186 (mp) REVERT: A 538 ILE cc_start: 0.7663 (mm) cc_final: 0.7454 (mm) REVERT: A 555 ILE cc_start: 0.7956 (tp) cc_final: 0.7648 (tp) REVERT: A 570 MET cc_start: 0.8379 (mmm) cc_final: 0.7548 (mmm) REVERT: A 591 ASP cc_start: 0.8127 (t0) cc_final: 0.7817 (t0) REVERT: A 602 GLU cc_start: 0.7130 (tt0) cc_final: 0.6889 (tt0) REVERT: A 614 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7978 (mt) REVERT: A 618 ASN cc_start: 0.8289 (t0) cc_final: 0.7960 (t0) REVERT: A 619 LYS cc_start: 0.8755 (tptp) cc_final: 0.8499 (tptm) REVERT: A 631 ARG cc_start: 0.7992 (ttm-80) cc_final: 0.7705 (ttp80) REVERT: A 677 ARG cc_start: 0.8209 (mtt90) cc_final: 0.7805 (mtt-85) REVERT: A 681 GLN cc_start: 0.7966 (mm110) cc_final: 0.7650 (mm110) REVERT: A 686 LYS cc_start: 0.8379 (ttmt) cc_final: 0.8097 (ttmm) REVERT: A 707 TYR cc_start: 0.8717 (OUTLIER) cc_final: 0.8222 (m-80) REVERT: A 735 VAL cc_start: 0.5056 (p) cc_final: 0.4403 (m) REVERT: A 761 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7936 (mp) REVERT: A 765 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.7170 (mtm-85) REVERT: A 791 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7124 (tm-30) REVERT: A 810 ILE cc_start: 0.8879 (mt) cc_final: 0.8572 (tt) REVERT: A 841 GLU cc_start: 0.7597 (mm-30) cc_final: 0.7318 (mm-30) REVERT: A 846 LYS cc_start: 0.8471 (mttm) cc_final: 0.7839 (mttm) REVERT: A 910 HIS cc_start: 0.6859 (OUTLIER) cc_final: 0.6512 (p90) REVERT: A 936 CYS cc_start: 0.8078 (t) cc_final: 0.7838 (t) REVERT: A 937 TRP cc_start: 0.8563 (t-100) cc_final: 0.8204 (t-100) REVERT: A 945 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7366 (ttm-80) REVERT: A 953 LEU cc_start: 0.7893 (tp) cc_final: 0.7637 (tp) REVERT: A 964 ILE cc_start: 0.7958 (pt) cc_final: 0.7703 (pt) REVERT: A 993 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7258 (m-30) REVERT: A 1002 MET cc_start: 0.7235 (mmt) cc_final: 0.6870 (mmt) REVERT: A 1011 TRP cc_start: 0.7057 (m100) cc_final: 0.6806 (m100) REVERT: A 1050 ILE cc_start: 0.8657 (mm) cc_final: 0.8448 (mt) outliers start: 28 outliers final: 16 residues processed: 208 average time/residue: 0.2545 time to fit residues: 65.5722 Evaluate side-chains 206 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 183 time to evaluate : 0.774 ------------------------------------------------------------------------------- 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 426 LEU Chi-restraints excluded: chain A residue 457 GLU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 707 TYR 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 817 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 993 ASP 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: 4.9990 chunk 50 optimal weight: 0.6980 chunk 34 optimal weight: 0.0070 chunk 7 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.5998 ------------------------------------------------------------------------------- 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: 0.7670 moved from start: 0.2891 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= 0.174 Angle : 0.521 8.117 8932 Z= 0.265 Chirality : 0.040 0.151 999 Planarity : 0.004 0.041 1050 Dihedral : 10.999 148.594 1024 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.32 % Favored : 96.54 % Rotamer: Outliers : 6.18 % Allowed : 24.43 % 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: 0.39 (0.32), residues: 722 helix: 1.20 (0.28), residues: 384 sheet: -0.68 (0.85), residues: 44 loop : -0.81 (0.36), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 940 HIS 0.012 0.002 HIS A 263 PHE 0.011 0.001 PHE A 847 TYR 0.011 0.001 TYR A 823 ARG 0.004 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 240 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7754 (ptm) cc_final: 0.7345 (ptm) REVERT: A 286 ASN cc_start: 0.8062 (m110) cc_final: 0.7778 (p0) REVERT: A 422 LYS cc_start: 0.8335 (tttt) cc_final: 0.7736 (ttmt) REVERT: A 424 GLU cc_start: 0.7898 (pm20) cc_final: 0.7565 (pm20) REVERT: A 444 GLU cc_start: 0.7663 (mp0) cc_final: 0.7455 (mp0) REVERT: A 468 LYS cc_start: 0.8729 (mmmm) cc_final: 0.8363 (mmmm) REVERT: A 479 GLU cc_start: 0.7274 (pt0) cc_final: 0.6960 (pp20) REVERT: A 485 LYS cc_start: 0.8536 (tttp) cc_final: 0.8067 (tptm) REVERT: A 486 GLU cc_start: 0.8329 (pt0) cc_final: 0.7900 (pt0) REVERT: A 494 LYS cc_start: 0.8372 (mtmt) cc_final: 0.7851 (ptmt) REVERT: A 502 GLU cc_start: 0.7401 (tp30) cc_final: 0.6912 (tp30) REVERT: A 505 LEU cc_start: 0.8612 (mp) cc_final: 0.8274 (mp) REVERT: A 516 LEU cc_start: 0.5606 (OUTLIER) cc_final: 0.5370 (mt) REVERT: A 555 ILE cc_start: 0.8140 (tp) cc_final: 0.7819 (tp) REVERT: A 570 MET cc_start: 0.8385 (mmm) cc_final: 0.7730 (mmm) REVERT: A 591 ASP cc_start: 0.8211 (t0) cc_final: 0.7948 (t0) REVERT: A 593 ASN cc_start: 0.8089 (t0) cc_final: 0.7636 (t0) REVERT: A 602 GLU cc_start: 0.7273 (tt0) cc_final: 0.6966 (tt0) REVERT: A 618 ASN cc_start: 0.8341 (t0) cc_final: 0.8033 (t0) REVERT: A 619 LYS cc_start: 0.8833 (tptp) cc_final: 0.8601 (tptm) REVERT: A 677 ARG cc_start: 0.8322 (mtt90) cc_final: 0.7832 (mtt-85) REVERT: A 681 GLN cc_start: 0.8058 (mm110) cc_final: 0.7712 (mm110) REVERT: A 686 LYS cc_start: 0.8423 (ttmt) cc_final: 0.8150 (ttmm) REVERT: A 707 TYR cc_start: 0.8773 (OUTLIER) cc_final: 0.8201 (m-80) REVERT: A 735 VAL cc_start: 0.5249 (p) cc_final: 0.4658 (m) REVERT: A 761 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8027 (mp) REVERT: A 765 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.7471 (mtm-85) REVERT: A 791 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7123 (tm-30) REVERT: A 810 ILE cc_start: 0.8890 (mt) cc_final: 0.8573 (tt) REVERT: A 836 PHE cc_start: 0.8366 (t80) cc_final: 0.8078 (t80) REVERT: A 841 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7367 (mm-30) REVERT: A 846 LYS cc_start: 0.8551 (mttm) cc_final: 0.7895 (mttm) REVERT: A 883 VAL cc_start: 0.8508 (t) cc_final: 0.8111 (t) REVERT: A 910 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6602 (p90) REVERT: A 936 CYS cc_start: 0.8129 (t) cc_final: 0.7853 (t) REVERT: A 937 TRP cc_start: 0.8612 (t-100) cc_final: 0.8086 (t-100) REVERT: A 953 LEU cc_start: 0.7893 (tp) cc_final: 0.7619 (tp) REVERT: A 993 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7237 (m-30) REVERT: A 1002 MET cc_start: 0.7275 (mmt) cc_final: 0.6912 (mmt) REVERT: A 1011 TRP cc_start: 0.7083 (m100) cc_final: 0.6827 (m100) REVERT: A 1050 ILE cc_start: 0.8650 (mm) cc_final: 0.8444 (mt) outliers start: 41 outliers final: 23 residues processed: 218 average time/residue: 0.2550 time to fit residues: 68.9862 Evaluate side-chains 225 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 196 time to evaluate : 0.627 ------------------------------------------------------------------------------- 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 495 LEU Chi-restraints excluded: chain A residue 516 LEU 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 582 VAL Chi-restraints excluded: chain A residue 606 ASP Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 802 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 969 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 ASP 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: 3.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 0.0020 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 36 optimal weight: 0.0010 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7677 moved from start: 0.3208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6555 Z= 0.162 Angle : 0.525 8.792 8932 Z= 0.267 Chirality : 0.040 0.141 999 Planarity : 0.004 0.040 1050 Dihedral : 10.930 148.648 1024 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.60 % Favored : 96.26 % Rotamer: Outliers : 4.83 % Allowed : 27.90 % Favored : 67.27 % 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: 1.22 (0.28), residues: 382 sheet: -0.58 (0.87), residues: 44 loop : -0.64 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 940 HIS 0.006 0.001 HIS A 263 PHE 0.011 0.001 PHE A 847 TYR 0.008 0.001 TYR A 823 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 234 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 272 MET cc_start: 0.7735 (ptm) cc_final: 0.7315 (ptm) REVERT: A 422 LYS cc_start: 0.8347 (tttt) cc_final: 0.7738 (ttmt) REVERT: A 424 GLU cc_start: 0.7950 (pm20) cc_final: 0.7625 (pm20) REVERT: A 468 LYS cc_start: 0.8765 (mmmm) cc_final: 0.8396 (mmmm) REVERT: A 485 LYS cc_start: 0.8529 (tttp) cc_final: 0.8098 (tptm) REVERT: A 486 GLU cc_start: 0.8449 (pt0) cc_final: 0.8164 (pt0) REVERT: A 502 GLU cc_start: 0.7370 (tp30) cc_final: 0.6927 (tp30) REVERT: A 505 LEU cc_start: 0.8605 (mp) cc_final: 0.8283 (mp) REVERT: A 516 LEU cc_start: 0.5727 (OUTLIER) cc_final: 0.5477 (mt) REVERT: A 555 ILE cc_start: 0.8103 (tp) cc_final: 0.7769 (tp) REVERT: A 570 MET cc_start: 0.8443 (mmm) cc_final: 0.7775 (mmm) REVERT: A 591 ASP cc_start: 0.8270 (t0) cc_final: 0.8032 (t0) REVERT: A 593 ASN cc_start: 0.8106 (t0) cc_final: 0.7667 (t0) REVERT: A 602 GLU cc_start: 0.7232 (tt0) cc_final: 0.6921 (tt0) REVERT: A 618 ASN cc_start: 0.8351 (t0) cc_final: 0.8060 (t0) REVERT: A 640 ASN cc_start: 0.7712 (OUTLIER) cc_final: 0.6996 (p0) REVERT: A 641 ILE cc_start: 0.7944 (mt) cc_final: 0.7701 (mp) REVERT: A 677 ARG cc_start: 0.8355 (mtt90) cc_final: 0.7884 (mtt-85) REVERT: A 681 GLN cc_start: 0.8125 (mm110) cc_final: 0.7803 (mm110) REVERT: A 686 LYS cc_start: 0.8450 (ttmt) cc_final: 0.8186 (ttmm) REVERT: A 735 VAL cc_start: 0.5232 (p) cc_final: 0.4669 (m) REVERT: A 761 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.8048 (mp) REVERT: A 765 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.7362 (mtm-85) REVERT: A 791 GLU cc_start: 0.7662 (tm-30) cc_final: 0.7116 (tm-30) REVERT: A 810 ILE cc_start: 0.8884 (mt) cc_final: 0.8569 (tt) REVERT: A 836 PHE cc_start: 0.8342 (t80) cc_final: 0.8086 (t80) REVERT: A 841 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7403 (mm-30) REVERT: A 846 LYS cc_start: 0.8574 (mttm) cc_final: 0.7896 (mttm) REVERT: A 910 HIS cc_start: 0.6945 (OUTLIER) cc_final: 0.6596 (p90) REVERT: A 937 TRP cc_start: 0.8623 (t-100) cc_final: 0.8038 (t-100) REVERT: A 945 ARG cc_start: 0.7650 (ttm-80) cc_final: 0.7414 (ttm-80) REVERT: A 953 LEU cc_start: 0.7816 (tp) cc_final: 0.7534 (tp) REVERT: A 993 ASP cc_start: 0.7549 (OUTLIER) cc_final: 0.7266 (m-30) REVERT: A 1002 MET cc_start: 0.7305 (mmt) cc_final: 0.6953 (mmt) REVERT: A 1011 TRP cc_start: 0.7071 (m100) cc_final: 0.6816 (m100) outliers start: 32 outliers final: 21 residues processed: 220 average time/residue: 0.2354 time to fit residues: 64.3958 Evaluate side-chains 226 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 199 time to evaluate : 0.689 ------------------------------------------------------------------------------- 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 516 LEU Chi-restraints excluded: chain A residue 523 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 614 LEU Chi-restraints excluded: chain A residue 640 ASN Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 802 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 969 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 59 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3613 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= 0.170 Angle : 0.532 8.417 8932 Z= 0.271 Chirality : 0.040 0.138 999 Planarity : 0.004 0.040 1050 Dihedral : 10.851 149.187 1024 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.02 % Favored : 95.84 % Rotamer: Outliers : 5.43 % Allowed : 28.81 % Favored : 65.76 % 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: 0.43 (0.32), residues: 722 helix: 1.23 (0.28), residues: 380 sheet: -0.69 (0.86), residues: 44 loop : -0.75 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 940 HIS 0.006 0.001 HIS A 263 PHE 0.011 0.001 PHE A 741 TYR 0.009 0.001 TYR A 823 ARG 0.003 0.000 ARG A 588 *********************** 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 235 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 199 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 422 LYS cc_start: 0.8353 (tttt) cc_final: 0.7828 (ttmt) REVERT: A 424 GLU cc_start: 0.7967 (pm20) cc_final: 0.7636 (pm20) REVERT: A 428 GLU cc_start: 0.7037 (tt0) cc_final: 0.6536 (tt0) REVERT: A 468 LYS cc_start: 0.8774 (mmmm) cc_final: 0.8399 (mmmm) REVERT: A 482 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.6674 (tp-100) REVERT: A 485 LYS cc_start: 0.8421 (tttp) cc_final: 0.8169 (tptm) REVERT: A 486 GLU cc_start: 0.8367 (pt0) cc_final: 0.8109 (pt0) REVERT: A 502 GLU cc_start: 0.7387 (tp30) cc_final: 0.7020 (tp30) REVERT: A 505 LEU cc_start: 0.8636 (mt) cc_final: 0.8330 (mp) REVERT: A 555 ILE cc_start: 0.8140 (tp) cc_final: 0.7817 (tp) REVERT: A 570 MET cc_start: 0.8401 (mmm) cc_final: 0.7653 (mmm) REVERT: A 591 ASP cc_start: 0.8317 (t0) cc_final: 0.8108 (t0) REVERT: A 593 ASN cc_start: 0.8105 (t0) cc_final: 0.7621 (t0) REVERT: A 602 GLU cc_start: 0.7264 (tt0) cc_final: 0.6921 (tt0) REVERT: A 618 ASN cc_start: 0.8354 (t0) cc_final: 0.8085 (t0) REVERT: A 677 ARG cc_start: 0.8415 (mtt90) cc_final: 0.8027 (mtt-85) REVERT: A 681 GLN cc_start: 0.8178 (mm110) cc_final: 0.7824 (mm110) REVERT: A 682 GLU cc_start: 0.8189 (tp30) cc_final: 0.7986 (tp30) REVERT: A 686 LYS cc_start: 0.8457 (ttmt) cc_final: 0.8195 (ttmm) REVERT: A 735 VAL cc_start: 0.5280 (p) cc_final: 0.4785 (m) REVERT: A 761 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.7997 (mp) REVERT: A 783 GLU cc_start: 0.7632 (tp30) cc_final: 0.7222 (tp30) REVERT: A 791 GLU cc_start: 0.7664 (tm-30) cc_final: 0.7140 (tm-30) REVERT: A 836 PHE cc_start: 0.8352 (t80) cc_final: 0.8140 (t80) REVERT: A 841 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7409 (mm-30) REVERT: A 846 LYS cc_start: 0.8568 (mttm) cc_final: 0.7896 (mttm) REVERT: A 910 HIS cc_start: 0.6953 (OUTLIER) cc_final: 0.6608 (p90) REVERT: A 937 TRP cc_start: 0.8631 (t-100) cc_final: 0.8078 (t-100) REVERT: A 953 LEU cc_start: 0.7760 (tp) cc_final: 0.7463 (tp) REVERT: A 984 THR cc_start: 0.7868 (p) cc_final: 0.7564 (t) REVERT: A 993 ASP cc_start: 0.7601 (OUTLIER) cc_final: 0.7095 (m-30) REVERT: A 1002 MET cc_start: 0.7318 (mmt) cc_final: 0.6964 (mmt) REVERT: A 1011 TRP cc_start: 0.7149 (m100) cc_final: 0.6881 (m100) outliers start: 36 outliers final: 27 residues processed: 217 average time/residue: 0.2789 time to fit residues: 75.7680 Evaluate side-chains 226 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 195 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 487 GLU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 582 VAL 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 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 817 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 964 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.0000 chunk 8 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 32 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6555 Z= 0.152 Angle : 0.527 8.538 8932 Z= 0.266 Chirality : 0.039 0.147 999 Planarity : 0.004 0.031 1050 Dihedral : 10.760 149.012 1024 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 6.18 % Allowed : 29.41 % Favored : 64.40 % 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: 0.43 (0.32), residues: 722 helix: 1.23 (0.28), residues: 378 sheet: -0.74 (0.85), residues: 44 loop : -0.74 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 940 HIS 0.006 0.001 HIS A 263 PHE 0.012 0.001 PHE A 741 TYR 0.009 0.001 TYR A 823 ARG 0.008 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 242 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 201 time to evaluate : 0.652 Fit side-chains revert: symmetry clash REVERT: A 424 GLU cc_start: 0.7955 (pm20) cc_final: 0.7618 (pm20) REVERT: A 428 GLU cc_start: 0.7014 (tt0) cc_final: 0.6524 (tt0) REVERT: A 468 LYS cc_start: 0.8762 (mmmm) cc_final: 0.8465 (mtmm) REVERT: A 482 GLN cc_start: 0.7660 (OUTLIER) cc_final: 0.7217 (tp40) REVERT: A 485 LYS cc_start: 0.8366 (tttp) cc_final: 0.8155 (tptm) REVERT: A 486 GLU cc_start: 0.8342 (pt0) cc_final: 0.8091 (pt0) REVERT: A 502 GLU cc_start: 0.7356 (tp30) cc_final: 0.7019 (tp30) REVERT: A 505 LEU cc_start: 0.8673 (mt) cc_final: 0.8383 (mp) REVERT: A 516 LEU cc_start: 0.6046 (OUTLIER) cc_final: 0.5760 (mt) REVERT: A 555 ILE cc_start: 0.8095 (tp) cc_final: 0.7761 (tp) REVERT: A 570 MET cc_start: 0.8400 (mmm) cc_final: 0.7618 (mmm) REVERT: A 593 ASN cc_start: 0.8113 (t0) cc_final: 0.7659 (t0) REVERT: A 602 GLU cc_start: 0.7208 (tt0) cc_final: 0.6892 (tt0) REVERT: A 618 ASN cc_start: 0.8382 (t0) cc_final: 0.8115 (t0) REVERT: A 677 ARG cc_start: 0.8399 (mtt90) cc_final: 0.7981 (mtt-85) REVERT: A 681 GLN cc_start: 0.8186 (mm110) cc_final: 0.7828 (mm110) REVERT: A 682 GLU cc_start: 0.8203 (tp30) cc_final: 0.7998 (tp30) REVERT: A 735 VAL cc_start: 0.5284 (p) cc_final: 0.4846 (m) REVERT: A 739 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8507 (mt0) REVERT: A 761 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7966 (mp) REVERT: A 783 GLU cc_start: 0.7588 (tp30) cc_final: 0.7245 (tp30) REVERT: A 791 GLU cc_start: 0.7679 (tm-30) cc_final: 0.7168 (tm-30) REVERT: A 810 ILE cc_start: 0.8845 (OUTLIER) cc_final: 0.8522 (tt) REVERT: A 834 MET cc_start: 0.7822 (mmm) cc_final: 0.7118 (tmm) REVERT: A 836 PHE cc_start: 0.8346 (t80) cc_final: 0.8134 (t80) REVERT: A 841 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7450 (mm-30) REVERT: A 846 LYS cc_start: 0.8576 (mttm) cc_final: 0.7897 (mttm) REVERT: A 910 HIS cc_start: 0.6928 (OUTLIER) cc_final: 0.6612 (p90) REVERT: A 937 TRP cc_start: 0.8623 (t-100) cc_final: 0.8084 (t-100) REVERT: A 953 LEU cc_start: 0.7702 (tp) cc_final: 0.7407 (tp) REVERT: A 984 THR cc_start: 0.7876 (p) cc_final: 0.7552 (t) REVERT: A 1002 MET cc_start: 0.7331 (mmt) cc_final: 0.6981 (mmt) REVERT: A 1011 TRP cc_start: 0.7142 (m100) cc_final: 0.6887 (m100) outliers start: 41 outliers final: 29 residues processed: 222 average time/residue: 0.2318 time to fit residues: 64.3475 Evaluate side-chains 231 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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 465 LEU Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 539 ASP Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 659 GLN 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 721 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 810 ILE Chi-restraints excluded: chain A residue 817 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 964 ILE Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 13 optimal weight: 0.0370 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.4114 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= 0.187 Angle : 0.544 8.519 8932 Z= 0.277 Chirality : 0.040 0.141 999 Planarity : 0.004 0.030 1050 Dihedral : 10.806 148.549 1024 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 5.58 % Allowed : 30.17 % 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: 0.29 (0.32), residues: 722 helix: 1.10 (0.28), residues: 382 sheet: -0.80 (0.85), residues: 44 loop : -0.80 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 940 HIS 0.006 0.001 HIS A 263 PHE 0.029 0.001 PHE A 781 TYR 0.008 0.001 TYR A 823 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 237 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 200 time to evaluate : 0.695 Fit side-chains revert: symmetry clash REVERT: A 424 GLU cc_start: 0.7975 (pm20) cc_final: 0.7634 (pm20) REVERT: A 428 GLU cc_start: 0.7104 (tt0) cc_final: 0.6605 (tt0) REVERT: A 468 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8387 (mmmm) REVERT: A 482 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7311 (tp40) REVERT: A 486 GLU cc_start: 0.8343 (pt0) cc_final: 0.8082 (pt0) REVERT: A 502 GLU cc_start: 0.7370 (tp30) cc_final: 0.7055 (tp30) REVERT: A 505 LEU cc_start: 0.8689 (mt) cc_final: 0.8415 (mp) REVERT: A 555 ILE cc_start: 0.8130 (tp) cc_final: 0.7792 (tp) REVERT: A 593 ASN cc_start: 0.8181 (t0) cc_final: 0.7701 (t0) REVERT: A 602 GLU cc_start: 0.7265 (tt0) cc_final: 0.6916 (tt0) REVERT: A 618 ASN cc_start: 0.8408 (t0) cc_final: 0.8164 (t0) REVERT: A 677 ARG cc_start: 0.8422 (mtt90) cc_final: 0.8008 (mtt-85) REVERT: A 681 GLN cc_start: 0.8202 (mm110) cc_final: 0.7862 (mm110) REVERT: A 735 VAL cc_start: 0.5408 (p) cc_final: 0.4993 (m) REVERT: A 739 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8612 (mt0) REVERT: A 741 PHE cc_start: 0.8311 (m-10) cc_final: 0.8063 (m-10) REVERT: A 761 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8112 (mp) REVERT: A 783 GLU cc_start: 0.7653 (tp30) cc_final: 0.7217 (tp30) REVERT: A 791 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7189 (tm-30) REVERT: A 810 ILE cc_start: 0.8834 (mt) cc_final: 0.8542 (tt) REVERT: A 834 MET cc_start: 0.7832 (mmm) cc_final: 0.7110 (tmm) REVERT: A 846 LYS cc_start: 0.8584 (mttm) cc_final: 0.7882 (mttm) REVERT: A 910 HIS cc_start: 0.6968 (OUTLIER) cc_final: 0.6619 (p90) REVERT: A 937 TRP cc_start: 0.8645 (t-100) cc_final: 0.8232 (t-100) REVERT: A 953 LEU cc_start: 0.7779 (tp) cc_final: 0.7488 (tp) REVERT: A 962 ARG cc_start: 0.8469 (ttp80) cc_final: 0.7940 (ttp80) REVERT: A 1002 MET cc_start: 0.7232 (mmt) cc_final: 0.6881 (mmt) REVERT: A 1011 TRP cc_start: 0.7150 (m100) cc_final: 0.6890 (m100) outliers start: 37 outliers final: 28 residues processed: 220 average time/residue: 0.2231 time to fit residues: 61.4494 Evaluate side-chains 231 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 199 time to evaluate : 0.717 ------------------------------------------------------------------------------- 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 465 LEU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 536 MET 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 721 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 817 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 964 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1014 ILE Chi-restraints excluded: chain A residue 1017 LYS Chi-restraints excluded: chain A residue 1046 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.0010 chunk 43 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7708 moved from start: 0.4322 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= 0.168 Angle : 0.557 9.744 8932 Z= 0.281 Chirality : 0.040 0.150 999 Planarity : 0.004 0.031 1050 Dihedral : 10.734 148.841 1024 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 5.28 % Allowed : 30.02 % Favored : 64.71 % 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: 0.44 (0.32), residues: 722 helix: 1.28 (0.28), residues: 371 sheet: -0.77 (0.85), residues: 44 loop : -0.73 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 899 HIS 0.006 0.001 HIS A 263 PHE 0.018 0.001 PHE A 574 TYR 0.009 0.001 TYR A 823 ARG 0.007 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 231 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: A 412 ARG cc_start: 0.8152 (mtp180) cc_final: 0.7931 (mtp85) REVERT: A 424 GLU cc_start: 0.7999 (pm20) cc_final: 0.7656 (pm20) REVERT: A 428 GLU cc_start: 0.7064 (tt0) cc_final: 0.6585 (tt0) REVERT: A 468 LYS cc_start: 0.8790 (mmmm) cc_final: 0.8384 (mmmm) REVERT: A 482 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7313 (tp40) REVERT: A 486 GLU cc_start: 0.8317 (pt0) cc_final: 0.8089 (pt0) REVERT: A 502 GLU cc_start: 0.7345 (tp30) cc_final: 0.7012 (tp30) REVERT: A 505 LEU cc_start: 0.8679 (mt) cc_final: 0.8404 (mp) REVERT: A 555 ILE cc_start: 0.8089 (tp) cc_final: 0.7754 (tp) REVERT: A 593 ASN cc_start: 0.8140 (t0) cc_final: 0.7673 (t0) REVERT: A 602 GLU cc_start: 0.7256 (tt0) cc_final: 0.6906 (tt0) REVERT: A 677 ARG cc_start: 0.8418 (mtt90) cc_final: 0.7982 (mtt-85) REVERT: A 681 GLN cc_start: 0.8191 (mm110) cc_final: 0.7817 (mm110) REVERT: A 735 VAL cc_start: 0.5370 (p) cc_final: 0.4964 (m) REVERT: A 739 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8568 (mt0) REVERT: A 741 PHE cc_start: 0.8242 (m-10) cc_final: 0.8015 (m-10) REVERT: A 761 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8106 (mp) REVERT: A 783 GLU cc_start: 0.7560 (tp30) cc_final: 0.7135 (tp30) REVERT: A 791 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7190 (tm-30) REVERT: A 810 ILE cc_start: 0.8814 (mt) cc_final: 0.8523 (tt) REVERT: A 834 MET cc_start: 0.7831 (mmm) cc_final: 0.7104 (tmm) REVERT: A 846 LYS cc_start: 0.8588 (mttm) cc_final: 0.7877 (mttm) REVERT: A 910 HIS cc_start: 0.6942 (OUTLIER) cc_final: 0.6608 (p90) REVERT: A 937 TRP cc_start: 0.8649 (t-100) cc_final: 0.8209 (t-100) REVERT: A 962 ARG cc_start: 0.8452 (ttp80) cc_final: 0.7935 (ttp80) REVERT: A 984 THR cc_start: 0.8068 (m) cc_final: 0.7572 (t) REVERT: A 1002 MET cc_start: 0.7307 (mmt) cc_final: 0.6914 (mmt) REVERT: A 1011 TRP cc_start: 0.7139 (m100) cc_final: 0.6879 (m100) outliers start: 35 outliers final: 27 residues processed: 215 average time/residue: 0.2429 time to fit residues: 64.6303 Evaluate side-chains 220 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 189 time to evaluate : 0.665 ------------------------------------------------------------------------------- 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 465 LEU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 536 MET Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 817 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 964 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.0050 chunk 48 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 67 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7713 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6555 Z= 0.178 Angle : 0.578 9.513 8932 Z= 0.292 Chirality : 0.040 0.150 999 Planarity : 0.004 0.032 1050 Dihedral : 10.760 148.643 1024 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.74 % Favored : 96.12 % Rotamer: Outliers : 4.98 % Allowed : 30.62 % Favored : 64.40 % 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: 0.42 (0.33), residues: 722 helix: 1.28 (0.28), residues: 373 sheet: -0.80 (0.85), residues: 44 loop : -0.77 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 899 HIS 0.006 0.001 HIS A 263 PHE 0.023 0.001 PHE A 574 TYR 0.008 0.001 TYR A 823 ARG 0.007 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 227 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 194 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 424 GLU cc_start: 0.8000 (pm20) cc_final: 0.7658 (pm20) REVERT: A 428 GLU cc_start: 0.7075 (tt0) cc_final: 0.6612 (tt0) REVERT: A 468 LYS cc_start: 0.8793 (mmmm) cc_final: 0.8375 (mmmm) REVERT: A 482 GLN cc_start: 0.7777 (OUTLIER) cc_final: 0.7448 (tp40) REVERT: A 486 GLU cc_start: 0.8356 (pt0) cc_final: 0.8130 (pt0) REVERT: A 502 GLU cc_start: 0.7351 (tp30) cc_final: 0.7019 (tp30) REVERT: A 505 LEU cc_start: 0.8683 (mt) cc_final: 0.8417 (mp) REVERT: A 555 ILE cc_start: 0.8093 (tp) cc_final: 0.7761 (tp) REVERT: A 575 ASN cc_start: 0.8468 (m-40) cc_final: 0.7937 (m110) REVERT: A 593 ASN cc_start: 0.8142 (t0) cc_final: 0.7667 (t0) REVERT: A 602 GLU cc_start: 0.7272 (tt0) cc_final: 0.6925 (tt0) REVERT: A 677 ARG cc_start: 0.8426 (mtt90) cc_final: 0.8076 (mtt-85) REVERT: A 735 VAL cc_start: 0.5340 (p) cc_final: 0.4948 (m) REVERT: A 739 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8590 (mt0) REVERT: A 761 ILE cc_start: 0.8435 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 783 GLU cc_start: 0.7561 (tp30) cc_final: 0.7146 (tp30) REVERT: A 791 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7230 (tm-30) REVERT: A 810 ILE cc_start: 0.8802 (mt) cc_final: 0.8518 (tt) REVERT: A 834 MET cc_start: 0.7815 (mmm) cc_final: 0.7036 (tmm) REVERT: A 846 LYS cc_start: 0.8589 (mttm) cc_final: 0.7879 (mttm) REVERT: A 910 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.6637 (p90) REVERT: A 937 TRP cc_start: 0.8647 (t-100) cc_final: 0.8234 (t-100) REVERT: A 958 LYS cc_start: 0.8399 (mttm) cc_final: 0.8001 (mttp) REVERT: A 962 ARG cc_start: 0.8468 (ttp80) cc_final: 0.7930 (ttp80) REVERT: A 984 THR cc_start: 0.8045 (m) cc_final: 0.7599 (t) REVERT: A 1002 MET cc_start: 0.7358 (mmt) cc_final: 0.6942 (mmt) REVERT: A 1011 TRP cc_start: 0.7145 (m100) cc_final: 0.6879 (m100) outliers start: 33 outliers final: 28 residues processed: 212 average time/residue: 0.2589 time to fit residues: 68.7033 Evaluate side-chains 223 residues out of total 663 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 191 time to evaluate : 0.714 ------------------------------------------------------------------------------- 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 465 LEU Chi-restraints excluded: chain A residue 474 ASP Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 487 GLU Chi-restraints excluded: chain A residue 495 LEU Chi-restraints excluded: chain A residue 534 SER Chi-restraints excluded: chain A residue 536 MET 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 699 LEU Chi-restraints excluded: chain A residue 707 TYR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 765 ARG Chi-restraints excluded: chain A residue 777 VAL Chi-restraints excluded: chain A residue 802 ILE Chi-restraints excluded: chain A residue 817 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 964 ILE Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 969 VAL Chi-restraints excluded: chain A residue 988 ILE Chi-restraints excluded: chain A residue 993 ASP Chi-restraints excluded: chain A residue 1017 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 20.0000 chunk 8 optimal weight: 0.0470 chunk 16 optimal weight: 0.7980 chunk 58 optimal weight: 0.0370 chunk 24 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 51 optimal weight: 0.1980 chunk 3 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 587 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 610 GLN ** A 640 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.139804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.116459 restraints weight = 10619.309| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.83 r_work: 0.3378 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6555 Z= 0.163 Angle : 0.567 9.482 8932 Z= 0.286 Chirality : 0.040 0.150 999 Planarity : 0.004 0.033 1050 Dihedral : 10.693 148.509 1024 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.88 % Favored : 95.98 % Rotamer: Outliers : 4.83 % Allowed : 30.92 % 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: 0.42 (0.33), residues: 722 helix: 1.29 (0.28), residues: 371 sheet: -0.72 (0.87), residues: 43 loop : -0.79 (0.36), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 899 HIS 0.006 0.001 HIS A 263 PHE 0.022 0.001 PHE A 741 TYR 0.009 0.001 TYR A 823 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: 2101.97 seconds wall clock time: 38 minutes 55.38 seconds (2335.38 seconds total)