Starting phenix.real_space_refine on Wed Mar 20 14:00:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/03_2024/7zmd_14795.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/03_2024/7zmd_14795.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/03_2024/7zmd_14795.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/03_2024/7zmd_14795.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/03_2024/7zmd_14795.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zmd_14795/03_2024/7zmd_14795.pdb" } resolution = 2.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9290 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 40 5.16 5 C 5883 2.51 5 N 1575 2.21 5 O 1796 1.98 5 H 9106 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 706": "OE1" <-> "OE2" Residue "A ASP 726": "OD1" <-> "OD2" Residue "A ASP 753": "OD1" <-> "OD2" Residue "A PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 757": "OD1" <-> "OD2" Residue "A ASP 770": "OD1" <-> "OD2" Residue "A PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 955": "OE1" <-> "OE2" Residue "A PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 989": "OE1" <-> "OE2" Residue "A TYR 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 1092": "OD1" <-> "OD2" Residue "B GLU 706": "OE1" <-> "OE2" Residue "B ASP 726": "OD1" <-> "OD2" Residue "B ASP 753": "OD1" <-> "OD2" Residue "B PHE 755": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 757": "OD1" <-> "OD2" Residue "B ASP 770": "OD1" <-> "OD2" Residue "B PHE 906": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 955": "OE1" <-> "OE2" Residue "B PHE 977": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 989": "OE1" <-> "OE2" Residue "B TYR 1043": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 1092": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18400 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 9205 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 25, 'TRANS': 570} Chain: "B" Number of atoms: 9195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 9195 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 25, 'TRANS': 569} Time building chain proxies: 8.63, per 1000 atoms: 0.47 Number of scatterers: 18400 At special positions: 0 Unit cell: (106.858, 119.554, 79.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 O 1796 8.00 N 1575 7.00 C 5883 6.00 H 9106 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 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: 14.41 Conformation dependent library (CDL) restraints added in 1.8 seconds 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2198 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 13 sheets defined 43.4% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 554 through 565 Processing helix chain 'A' and resid 608 through 613 Processing helix chain 'A' and resid 615 through 622 Processing helix chain 'A' and resid 623 through 640 Processing helix chain 'A' and resid 643 through 648 removed outlier: 4.589A pdb=" N CYS A 648 " --> pdb=" O PRO A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 4.123A pdb=" N ALA A 674 " --> pdb=" O TYR A 670 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LEU A 677 " --> pdb=" O ILE A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 695 through 710 Processing helix chain 'A' and resid 726 through 736 removed outlier: 4.309A pdb=" N TYR A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 733 " --> pdb=" O HIS A 729 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 736 " --> pdb=" O LYS A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 769 through 776 Processing helix chain 'A' and resid 801 through 817 Processing helix chain 'A' and resid 819 through 821 No H-bonds generated for 'chain 'A' and resid 819 through 821' Processing helix chain 'A' and resid 835 through 850 removed outlier: 3.829A pdb=" N ILE A 839 " --> pdb=" O LEU A 835 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 868 Processing helix chain 'A' and resid 870 through 872 No H-bonds generated for 'chain 'A' and resid 870 through 872' Processing helix chain 'A' and resid 873 through 889 Processing helix chain 'A' and resid 905 through 909 Processing helix chain 'A' and resid 926 through 930 removed outlier: 3.653A pdb=" N GLY A 929 " --> pdb=" O GLU A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1002 Processing helix chain 'A' and resid 1004 through 1006 No H-bonds generated for 'chain 'A' and resid 1004 through 1006' Processing helix chain 'A' and resid 1007 through 1018 Processing helix chain 'A' and resid 1032 through 1045 Processing helix chain 'A' and resid 1062 through 1071 removed outlier: 4.025A pdb=" N ASP A1071 " --> pdb=" O ILE A1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 1071 through 1084 removed outlier: 4.170A pdb=" N GLU A1075 " --> pdb=" O ASP A1071 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1095 Processing helix chain 'A' and resid 1101 through 1106 removed outlier: 3.609A pdb=" N LYS A1104 " --> pdb=" O ASP A1101 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 565 Processing helix chain 'B' and resid 608 through 613 Processing helix chain 'B' and resid 615 through 622 Processing helix chain 'B' and resid 623 through 640 Processing helix chain 'B' and resid 643 through 648 removed outlier: 4.588A pdb=" N CYS B 648 " --> pdb=" O PRO B 644 " (cutoff:3.500A) Processing helix chain 'B' and resid 670 through 681 removed outlier: 4.122A pdb=" N ALA B 674 " --> pdb=" O TYR B 670 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU B 677 " --> pdb=" O ILE B 673 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 694 No H-bonds generated for 'chain 'B' and resid 692 through 694' Processing helix chain 'B' and resid 695 through 710 Processing helix chain 'B' and resid 726 through 736 removed outlier: 4.309A pdb=" N TYR B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU B 733 " --> pdb=" O HIS B 729 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU B 736 " --> pdb=" O LYS B 732 " (cutoff:3.500A) Processing helix chain 'B' and resid 769 through 776 Processing helix chain 'B' and resid 801 through 817 Processing helix chain 'B' and resid 819 through 821 No H-bonds generated for 'chain 'B' and resid 819 through 821' Processing helix chain 'B' and resid 835 through 850 removed outlier: 3.829A pdb=" N ILE B 839 " --> pdb=" O LEU B 835 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 868 Processing helix chain 'B' and resid 870 through 872 No H-bonds generated for 'chain 'B' and resid 870 through 872' Processing helix chain 'B' and resid 873 through 889 Processing helix chain 'B' and resid 905 through 909 Processing helix chain 'B' and resid 983 through 1002 Processing helix chain 'B' and resid 1004 through 1006 No H-bonds generated for 'chain 'B' and resid 1004 through 1006' Processing helix chain 'B' and resid 1007 through 1018 Processing helix chain 'B' and resid 1032 through 1045 Processing helix chain 'B' and resid 1062 through 1071 removed outlier: 4.024A pdb=" N ASP B1071 " --> pdb=" O ILE B1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 1071 through 1084 removed outlier: 4.169A pdb=" N GLU B1075 " --> pdb=" O ASP B1071 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1095 Processing helix chain 'B' and resid 1101 through 1106 removed outlier: 3.609A pdb=" N LYS B1104 " --> pdb=" O ASP B1101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 823 through 827 removed outlier: 6.926A pdb=" N ILE A 937 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR A 825 " --> pdb=" O ILE A 937 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASN A 949 " --> pdb=" O MET A 788 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N MET A 788 " --> pdb=" O ASN A 949 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS A 951 " --> pdb=" O SER A 786 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N SER A 786 " --> pdb=" O HIS A 951 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE A 953 " --> pdb=" O LYS A 784 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY A 781 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 765 " --> pdb=" O ILE A 543 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU A 545 " --> pdb=" O ALA A 763 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ALA A 763 " --> pdb=" O LEU A 545 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLY A 547 " --> pdb=" O VAL A 761 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL A 761 " --> pdb=" O GLY A 547 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL A 688 " --> pdb=" O VAL A 653 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 655 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL A 690 " --> pdb=" O VAL A 655 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 657 " --> pdb=" O VAL A 690 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N VAL B 688 " --> pdb=" O VAL B 653 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL B 655 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL B 690 " --> pdb=" O VAL B 655 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL B 657 " --> pdb=" O VAL B 690 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 761 " --> pdb=" O GLY B 547 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLY B 547 " --> pdb=" O VAL B 761 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N ALA B 763 " --> pdb=" O LEU B 545 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU B 545 " --> pdb=" O ALA B 763 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N VAL B 765 " --> pdb=" O ILE B 543 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY B 781 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE B 953 " --> pdb=" O LYS B 784 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N SER B 786 " --> pdb=" O HIS B 951 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS B 951 " --> pdb=" O SER B 786 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N MET B 788 " --> pdb=" O ASN B 949 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN B 949 " --> pdb=" O MET B 788 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE B 937 " --> pdb=" O VAL B 823 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR B 825 " --> pdb=" O ILE B 937 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 570 through 571 Processing sheet with id=AA3, first strand: chain 'A' and resid 606 through 607 Processing sheet with id=AA4, first strand: chain 'A' and resid 858 through 860 removed outlier: 6.209A pdb=" N CYS A 858 " --> pdb=" O VAL A 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AA6, first strand: chain 'A' and resid 924 through 925 removed outlier: 3.567A pdb=" N VAL A 925 " --> pdb=" O ASN A 932 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 975 through 981 removed outlier: 3.505A pdb=" N ALA A1030 " --> pdb=" O ALA A 975 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A1056 " --> pdb=" O ARG A1025 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A1027 " --> pdb=" O TYR A1054 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 570 through 571 Processing sheet with id=AA9, first strand: chain 'B' and resid 606 through 607 Processing sheet with id=AB1, first strand: chain 'B' and resid 858 through 860 removed outlier: 6.209A pdb=" N CYS B 858 " --> pdb=" O VAL B 912 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 890 through 891 Processing sheet with id=AB3, first strand: chain 'B' and resid 924 through 925 removed outlier: 3.566A pdb=" N VAL B 925 " --> pdb=" O ASN B 932 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 975 through 981 removed outlier: 3.504A pdb=" N ALA B1030 " --> pdb=" O ALA B 975 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B1056 " --> pdb=" O ARG B1025 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B1027 " --> pdb=" O TYR B1054 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.50 Time building geometry restraints manager: 14.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9094 1.03 - 1.23: 12 1.23 - 1.42: 3993 1.42 - 1.62: 5435 1.62 - 1.81: 66 Bond restraints: 18600 Sorted by residual: bond pdb=" CD ARG B1025 " pdb=" NE ARG B1025 " ideal model delta sigma weight residual 1.458 1.444 0.014 1.40e-02 5.10e+03 9.67e-01 bond pdb=" NH1 ARG A1025 " pdb="HH12 ARG A1025 " ideal model delta sigma weight residual 0.860 0.840 0.020 2.00e-02 2.50e+03 9.60e-01 bond pdb=" CD ARG A1025 " pdb=" NE ARG A1025 " ideal model delta sigma weight residual 1.458 1.445 0.013 1.40e-02 5.10e+03 9.14e-01 bond pdb=" C TYR A 664 " pdb=" N PRO A 665 " ideal model delta sigma weight residual 1.336 1.346 -0.010 1.08e-02 8.57e+03 9.06e-01 bond pdb=" C TYR B 664 " pdb=" N PRO B 665 " ideal model delta sigma weight residual 1.336 1.346 -0.010 1.08e-02 8.57e+03 8.84e-01 ... (remaining 18595 not shown) Histogram of bond angle deviations from ideal: 71.69 - 84.76: 23 84.76 - 97.84: 0 97.84 - 110.91: 19949 110.91 - 123.99: 12375 123.99 - 137.06: 1267 Bond angle restraints: 33614 Sorted by residual: angle pdb=" N VAL A 536 " pdb=" CA VAL A 536 " pdb=" HA VAL A 536 " ideal model delta sigma weight residual 110.00 72.38 37.62 3.00e+00 1.11e-01 1.57e+02 angle pdb=" C VAL A 536 " pdb=" CA VAL A 536 " pdb=" HA VAL A 536 " ideal model delta sigma weight residual 109.00 71.69 37.31 3.00e+00 1.11e-01 1.55e+02 angle pdb=" OG1 THR A 699 " pdb=" CB THR A 699 " pdb=" HB THR A 699 " ideal model delta sigma weight residual 109.00 74.04 34.96 3.00e+00 1.11e-01 1.36e+02 angle pdb=" CG2 THR A 699 " pdb=" CB THR A 699 " pdb=" HB THR A 699 " ideal model delta sigma weight residual 108.00 73.69 34.31 3.00e+00 1.11e-01 1.31e+02 angle pdb=" OG1 THR A 669 " pdb=" CB THR A 669 " pdb=" HB THR A 669 " ideal model delta sigma weight residual 109.00 75.45 33.55 3.00e+00 1.11e-01 1.25e+02 ... (remaining 33609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 7936 15.90 - 31.80: 567 31.80 - 47.70: 161 47.70 - 63.60: 87 63.60 - 79.50: 16 Dihedral angle restraints: 8767 sinusoidal: 4750 harmonic: 4017 Sorted by residual: dihedral pdb=" CD ARG B1025 " pdb=" NE ARG B1025 " pdb=" CZ ARG B1025 " pdb=" NH1 ARG B1025 " ideal model delta sinusoidal sigma weight residual 0.00 51.82 -51.82 1 1.00e+01 1.00e-02 3.67e+01 dihedral pdb=" CD ARG A1025 " pdb=" NE ARG A1025 " pdb=" CZ ARG A1025 " pdb=" NH1 ARG A1025 " ideal model delta sinusoidal sigma weight residual 0.00 51.80 -51.80 1 1.00e+01 1.00e-02 3.66e+01 dihedral pdb=" CA LEU B 736 " pdb=" C LEU B 736 " pdb=" N THR B 737 " pdb=" CA THR B 737 " ideal model delta harmonic sigma weight residual 180.00 160.34 19.66 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 8764 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.342: 1405 0.342 - 0.684: 4 0.684 - 1.026: 0 1.026 - 1.368: 0 1.368 - 1.710: 2 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CG LEU A 826 " pdb=" CB LEU A 826 " pdb=" CD1 LEU A 826 " pdb=" CD2 LEU A 826 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.31e+01 chirality pdb=" CG LEU B 826 " pdb=" CB LEU B 826 " pdb=" CD1 LEU B 826 " pdb=" CD2 LEU B 826 " both_signs ideal model delta sigma weight residual False -2.59 -0.88 -1.71 2.00e-01 2.50e+01 7.27e+01 chirality pdb=" CB THR B 699 " pdb=" CA THR B 699 " pdb=" OG1 THR B 699 " pdb=" CG2 THR B 699 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.71e+00 ... (remaining 1408 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A1025 " -0.820 9.50e-02 1.11e+02 2.74e-01 8.62e+01 pdb=" NE ARG A1025 " 0.060 2.00e-02 2.50e+03 pdb=" CZ ARG A1025 " -0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A1025 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A1025 " -0.012 2.00e-02 2.50e+03 pdb="HH11 ARG A1025 " -0.006 2.00e-02 2.50e+03 pdb="HH12 ARG A1025 " 0.023 2.00e-02 2.50e+03 pdb="HH21 ARG A1025 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A1025 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B1025 " -0.835 9.50e-02 1.11e+02 2.79e-01 8.52e+01 pdb=" NE ARG B1025 " 0.052 2.00e-02 2.50e+03 pdb=" CZ ARG B1025 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B1025 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG B1025 " -0.008 2.00e-02 2.50e+03 pdb="HH11 ARG B1025 " 0.004 2.00e-02 2.50e+03 pdb="HH12 ARG B1025 " 0.013 2.00e-02 2.50e+03 pdb="HH21 ARG B1025 " -0.004 2.00e-02 2.50e+03 pdb="HH22 ARG B1025 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 767 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.16e+00 pdb=" N PRO B 768 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO B 768 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 768 " 0.020 5.00e-02 4.00e+02 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.14: 535 2.14 - 2.76: 34481 2.76 - 3.37: 51267 3.37 - 3.99: 67559 3.99 - 4.60: 107523 Nonbonded interactions: 261365 Sorted by model distance: nonbonded pdb="HH21 ARG B 986 " pdb=" OE2 GLU B 989 " model vdw 1.531 1.850 nonbonded pdb="HH21 ARG A 986 " pdb=" OE2 GLU A 989 " model vdw 1.531 1.850 nonbonded pdb=" HE3 LYS A1086 " pdb=" HZ2 LYS A1086 " model vdw 1.598 1.816 nonbonded pdb=" HE2 LYS A1086 " pdb=" HZ3 LYS A1086 " model vdw 1.599 1.816 nonbonded pdb=" HB THR A 669 " pdb="HG23 THR A 669 " model vdw 1.628 1.952 ... (remaining 261360 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 536 through 1130) selection = chain 'B' } 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.290 Extract box with map and model: 7.890 Check model and map are aligned: 0.300 Set scattering table: 0.170 Process input model: 59.250 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 82.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 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 : 0.002 0.030 9494 Z= 0.135 Angle : 0.522 10.126 12870 Z= 0.261 Chirality : 0.081 1.710 1411 Planarity : 0.013 0.370 1681 Dihedral : 13.129 79.496 3486 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % 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: 0.93 (0.25), residues: 1187 helix: 1.91 (0.25), residues: 412 sheet: 0.95 (0.46), residues: 138 loop : -0.30 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1081 HIS 0.004 0.001 HIS A1049 PHE 0.006 0.001 PHE B 857 TYR 0.008 0.001 TYR B 642 ARG 0.008 0.001 ARG A1025 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASP cc_start: 0.7711 (m-30) cc_final: 0.7376 (m-30) REVERT: B 854 ASP cc_start: 0.7771 (m-30) cc_final: 0.7416 (m-30) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 2.8603 time to fit residues: 438.1290 Evaluate side-chains 98 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 35 optimal weight: 0.0970 chunk 56 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 GLN B 853 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9494 Z= 0.235 Angle : 0.616 23.714 12870 Z= 0.306 Chirality : 0.093 1.724 1411 Planarity : 0.004 0.037 1681 Dihedral : 4.034 21.713 1277 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.81 % Allowed : 9.38 % Favored : 89.81 % 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: 0.80 (0.25), residues: 1187 helix: 1.73 (0.25), residues: 422 sheet: 0.41 (0.41), residues: 160 loop : -0.25 (0.26), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A1081 HIS 0.003 0.001 HIS B 702 PHE 0.010 0.002 PHE A 911 TYR 0.010 0.001 TYR A 642 ARG 0.004 0.000 ARG B1025 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASP cc_start: 0.7742 (m-30) cc_final: 0.7372 (m-30) REVERT: B 854 ASP cc_start: 0.7783 (m-30) cc_final: 0.7433 (m-30) outliers start: 8 outliers final: 4 residues processed: 115 average time/residue: 2.6015 time to fit residues: 321.3959 Evaluate side-chains 106 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 931 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 0.0010 chunk 86 optimal weight: 0.9980 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 751 GLN A 853 GLN ** A 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1103 ASN B 751 GLN B 853 GLN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1103 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9494 Z= 0.189 Angle : 0.586 25.329 12870 Z= 0.284 Chirality : 0.092 1.736 1411 Planarity : 0.004 0.049 1681 Dihedral : 3.870 20.192 1277 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.61 % Allowed : 10.80 % Favored : 88.60 % 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: 0.88 (0.24), residues: 1187 helix: 1.82 (0.25), residues: 421 sheet: 0.64 (0.43), residues: 140 loop : -0.25 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 559 HIS 0.002 0.001 HIS A 888 PHE 0.009 0.001 PHE A 629 TYR 0.009 0.001 TYR B 988 ARG 0.006 0.000 ARG A1025 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 109 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 854 ASP cc_start: 0.7924 (m-30) cc_final: 0.7562 (m-30) REVERT: B 850 LYS cc_start: 0.7562 (tttt) cc_final: 0.6764 (mttt) REVERT: B 854 ASP cc_start: 0.7816 (m-30) cc_final: 0.7481 (m-30) outliers start: 6 outliers final: 2 residues processed: 114 average time/residue: 2.7369 time to fit residues: 334.3114 Evaluate side-chains 105 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 103 time to evaluate : 1.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain B residue 826 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN A 856 GLN A 999 GLN B 751 GLN ** B 856 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 999 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9494 Z= 0.327 Angle : 0.665 26.011 12870 Z= 0.327 Chirality : 0.097 1.767 1411 Planarity : 0.004 0.038 1681 Dihedral : 4.312 20.102 1277 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.72 % Allowed : 11.20 % Favored : 87.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1187 helix: 1.47 (0.25), residues: 420 sheet: -0.11 (0.39), residues: 182 loop : -0.42 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 920 HIS 0.003 0.001 HIS B 729 PHE 0.013 0.002 PHE B 911 TYR 0.008 0.002 TYR A1126 ARG 0.008 0.001 ARG A1025 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 621 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7222 (mp0) REVERT: A 840 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7353 (tt0) REVERT: A 850 LYS cc_start: 0.7603 (tttt) cc_final: 0.6882 (mttt) REVERT: A 854 ASP cc_start: 0.7924 (m-30) cc_final: 0.7629 (m-30) REVERT: A 1000 GLU cc_start: 0.7167 (mt-10) cc_final: 0.6961 (pt0) REVERT: A 1044 VAL cc_start: 0.7200 (OUTLIER) cc_final: 0.6974 (t) REVERT: B 621 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7248 (mp0) REVERT: B 850 LYS cc_start: 0.7603 (tttt) cc_final: 0.6878 (mttt) REVERT: B 854 ASP cc_start: 0.7796 (m-30) cc_final: 0.7510 (m-30) REVERT: B 1044 VAL cc_start: 0.7208 (OUTLIER) cc_final: 0.6979 (t) outliers start: 17 outliers final: 4 residues processed: 111 average time/residue: 2.7659 time to fit residues: 328.1421 Evaluate side-chains 107 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 621 GLU Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1044 VAL Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 1044 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 817 ASN A 853 GLN A 999 GLN B 751 GLN B 817 ASN B 856 GLN B 999 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9494 Z= 0.197 Angle : 0.603 26.033 12870 Z= 0.291 Chirality : 0.094 1.748 1411 Planarity : 0.004 0.039 1681 Dihedral : 4.007 18.576 1277 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.11 % Allowed : 12.41 % Favored : 86.48 % 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: 0.56 (0.25), residues: 1187 helix: 1.69 (0.24), residues: 416 sheet: -0.18 (0.38), residues: 193 loop : -0.35 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 559 HIS 0.002 0.001 HIS B 869 PHE 0.011 0.001 PHE B 629 TYR 0.008 0.001 TYR B 988 ARG 0.004 0.000 ARG A1025 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 105 time to evaluate : 1.461 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 850 LYS cc_start: 0.7532 (tttt) cc_final: 0.6814 (mtmt) REVERT: A 854 ASP cc_start: 0.7785 (m-30) cc_final: 0.7540 (m-30) REVERT: B 850 LYS cc_start: 0.7532 (tttt) cc_final: 0.6782 (mttt) REVERT: B 854 ASP cc_start: 0.7734 (m-30) cc_final: 0.7486 (m-30) outliers start: 11 outliers final: 4 residues processed: 112 average time/residue: 2.6758 time to fit residues: 320.8682 Evaluate side-chains 101 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 97 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 925 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 2.9990 chunk 102 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 0.3980 chunk 28 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 94 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 9 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 853 GLN B 999 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9494 Z= 0.177 Angle : 0.592 26.060 12870 Z= 0.284 Chirality : 0.094 1.739 1411 Planarity : 0.004 0.037 1681 Dihedral : 3.877 18.926 1277 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.41 % Allowed : 12.21 % Favored : 86.38 % 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: 0.66 (0.25), residues: 1187 helix: 1.78 (0.24), residues: 422 sheet: -0.17 (0.37), residues: 204 loop : -0.32 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 559 HIS 0.001 0.001 HIS B 702 PHE 0.010 0.001 PHE B 629 TYR 0.008 0.001 TYR A 988 ARG 0.002 0.000 ARG A1025 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 1.465 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 850 LYS cc_start: 0.7495 (tttt) cc_final: 0.6832 (ttmt) REVERT: A 854 ASP cc_start: 0.7768 (m-30) cc_final: 0.7546 (m-30) REVERT: A 1055 ARG cc_start: 0.7353 (OUTLIER) cc_final: 0.6533 (mtt-85) REVERT: B 621 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: B 850 LYS cc_start: 0.7506 (tttt) cc_final: 0.6842 (ttmt) REVERT: B 854 ASP cc_start: 0.7739 (m-30) cc_final: 0.7535 (m-30) outliers start: 14 outliers final: 5 residues processed: 110 average time/residue: 2.8919 time to fit residues: 339.0549 Evaluate side-chains 101 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 94 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 1055 ARG Chi-restraints excluded: chain B residue 621 GLU Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 925 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 113 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 817 ASN A 999 GLN B 817 ASN B 999 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9494 Z= 0.260 Angle : 0.628 26.203 12870 Z= 0.305 Chirality : 0.096 1.768 1411 Planarity : 0.004 0.041 1681 Dihedral : 4.090 18.523 1277 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.72 % Allowed : 12.21 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.24), residues: 1187 helix: 1.58 (0.24), residues: 428 sheet: -0.06 (0.38), residues: 182 loop : -0.59 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A1102 HIS 0.003 0.001 HIS B 729 PHE 0.013 0.002 PHE B 629 TYR 0.008 0.001 TYR B 988 ARG 0.004 0.000 ARG A1025 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 840 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7939 (tm-30) REVERT: A 850 LYS cc_start: 0.7380 (tttt) cc_final: 0.6605 (mttt) REVERT: A 854 ASP cc_start: 0.7781 (m-30) cc_final: 0.7575 (m-30) REVERT: A 1055 ARG cc_start: 0.7293 (OUTLIER) cc_final: 0.6387 (mtt-85) REVERT: B 770 ASP cc_start: 0.7544 (p0) cc_final: 0.7310 (p0) REVERT: B 850 LYS cc_start: 0.7344 (tttt) cc_final: 0.6612 (mttt) REVERT: B 1055 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6362 (mtt-85) outliers start: 17 outliers final: 7 residues processed: 110 average time/residue: 3.1212 time to fit residues: 364.3112 Evaluate side-chains 103 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 1055 ARG Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 1055 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN B 999 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9494 Z= 0.212 Angle : 0.611 26.163 12870 Z= 0.294 Chirality : 0.095 1.753 1411 Planarity : 0.004 0.045 1681 Dihedral : 4.002 18.815 1277 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.72 % Allowed : 12.01 % Favored : 86.28 % 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: 0.46 (0.24), residues: 1187 helix: 1.67 (0.24), residues: 428 sheet: -0.05 (0.38), residues: 182 loop : -0.60 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 559 HIS 0.003 0.001 HIS B 869 PHE 0.011 0.001 PHE B 629 TYR 0.008 0.001 TYR A 988 ARG 0.003 0.000 ARG A1025 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 840 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7885 (tm-30) REVERT: A 850 LYS cc_start: 0.7331 (tttt) cc_final: 0.6681 (ttmt) REVERT: A 854 ASP cc_start: 0.7799 (m-30) cc_final: 0.7570 (m-30) REVERT: A 926 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6125 (mm-30) REVERT: A 1055 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6391 (mtt-85) REVERT: B 770 ASP cc_start: 0.7523 (p0) cc_final: 0.7260 (p0) REVERT: B 840 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7151 (tt0) REVERT: B 850 LYS cc_start: 0.7292 (tttt) cc_final: 0.6665 (ttmt) outliers start: 17 outliers final: 7 residues processed: 110 average time/residue: 3.0709 time to fit residues: 359.1680 Evaluate side-chains 106 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 95 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 925 VAL Chi-restraints excluded: chain A residue 926 GLU Chi-restraints excluded: chain A residue 1055 ARG Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 840 GLU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 931 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 69 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 817 ASN B 751 GLN B 817 ASN B 999 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 9494 Z= 0.311 Angle : 0.658 26.259 12870 Z= 0.322 Chirality : 0.097 1.783 1411 Planarity : 0.004 0.047 1681 Dihedral : 4.261 18.931 1277 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.61 % Allowed : 12.41 % Favored : 85.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.24), residues: 1187 helix: 1.53 (0.24), residues: 428 sheet: -0.06 (0.38), residues: 182 loop : -0.70 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1102 HIS 0.003 0.001 HIS B 869 PHE 0.013 0.002 PHE B 629 TYR 0.009 0.002 TYR B1054 ARG 0.005 0.001 ARG A1025 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 99 time to evaluate : 1.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 840 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: A 850 LYS cc_start: 0.7404 (tttt) cc_final: 0.6649 (mttt) REVERT: A 854 ASP cc_start: 0.7800 (m-30) cc_final: 0.7556 (m-30) REVERT: A 1055 ARG cc_start: 0.7320 (OUTLIER) cc_final: 0.6312 (mtt-85) REVERT: B 840 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7216 (tt0) REVERT: B 850 LYS cc_start: 0.7430 (tttt) cc_final: 0.6762 (ttmt) REVERT: B 854 ASP cc_start: 0.7877 (m-30) cc_final: 0.7675 (m-30) REVERT: B 1055 ARG cc_start: 0.7310 (OUTLIER) cc_final: 0.6304 (mtt-85) outliers start: 16 outliers final: 8 residues processed: 107 average time/residue: 3.1762 time to fit residues: 360.6590 Evaluate side-chains 108 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 96 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 931 THR Chi-restraints excluded: chain A residue 1055 ARG Chi-restraints excluded: chain B residue 736 LEU Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 840 GLU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 931 THR Chi-restraints excluded: chain B residue 1055 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 999 GLN B 795 ASN B 999 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9494 Z= 0.199 Angle : 0.612 26.189 12870 Z= 0.295 Chirality : 0.095 1.759 1411 Planarity : 0.004 0.049 1681 Dihedral : 4.032 18.520 1277 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.21 % Allowed : 13.42 % Favored : 85.37 % 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 (0.24), residues: 1187 helix: 1.72 (0.24), residues: 428 sheet: -0.10 (0.38), residues: 187 loop : -0.64 (0.26), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 559 HIS 0.004 0.001 HIS A 869 PHE 0.011 0.001 PHE B 629 TYR 0.008 0.001 TYR B 988 ARG 0.003 0.000 ARG A1025 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2374 Ramachandran restraints generated. 1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 840 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7798 (tm-30) REVERT: A 850 LYS cc_start: 0.7354 (tttt) cc_final: 0.6702 (ttmt) REVERT: A 854 ASP cc_start: 0.7775 (m-30) cc_final: 0.7553 (m-30) REVERT: A 1055 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.6250 (mtt-85) REVERT: B 850 LYS cc_start: 0.7346 (tttt) cc_final: 0.6694 (ttmt) REVERT: B 1055 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6228 (mtt-85) outliers start: 12 outliers final: 5 residues processed: 110 average time/residue: 3.2660 time to fit residues: 380.4898 Evaluate side-chains 107 residues out of total 991 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 99 time to evaluate : 1.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 777 ASP Chi-restraints excluded: chain A residue 826 LEU Chi-restraints excluded: chain A residue 840 GLU Chi-restraints excluded: chain A residue 1055 ARG Chi-restraints excluded: chain B residue 777 ASP Chi-restraints excluded: chain B residue 826 LEU Chi-restraints excluded: chain B residue 925 VAL Chi-restraints excluded: chain B residue 1055 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 817 ASN A 999 GLN B 817 ASN B 999 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.159656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132739 restraints weight = 29217.136| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 1.63 r_work: 0.3381 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9494 Z= 0.215 Angle : 0.616 26.096 12870 Z= 0.298 Chirality : 0.095 1.758 1411 Planarity : 0.004 0.048 1681 Dihedral : 4.011 19.025 1277 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.31 % Allowed : 13.42 % Favored : 85.27 % 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: 0.47 (0.24), residues: 1187 helix: 1.76 (0.24), residues: 428 sheet: 0.02 (0.39), residues: 182 loop : -0.69 (0.26), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 559 HIS 0.002 0.001 HIS B 869 PHE 0.012 0.001 PHE B 629 TYR 0.009 0.001 TYR B 988 ARG 0.003 0.000 ARG B1025 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6840.82 seconds wall clock time: 119 minutes 50.31 seconds (7190.31 seconds total)