Starting phenix.real_space_refine on Mon Mar 11 02:09:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfz_22857/03_2024/7kfz_22857_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfz_22857/03_2024/7kfz_22857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfz_22857/03_2024/7kfz_22857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfz_22857/03_2024/7kfz_22857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfz_22857/03_2024/7kfz_22857_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kfz_22857/03_2024/7kfz_22857_updated.pdb" } resolution = 3.47 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= 0.002 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 3 5.49 5 Mg 1 5.21 5 S 27 5.16 5 C 4176 2.51 5 N 1134 2.21 5 O 1251 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 41": "NH1" <-> "NH2" Residue "A GLU 49": "OE1" <-> "OE2" Residue "A ASP 69": "OD1" <-> "OD2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 97": "NH1" <-> "NH2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A GLU 168": "OE1" <-> "OE2" Residue "B ARG 568": "NH1" <-> "NH2" Residue "B TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 581": "OD1" <-> "OD2" Residue "B GLU 583": "OE1" <-> "OE2" Residue "B TYR 618": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 623": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 627": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 652": "OE1" <-> "OE2" Residue "B GLU 657": "OE1" <-> "OE2" Residue "B ARG 688": "NH1" <-> "NH2" Residue "B ARG 694": "NH1" <-> "NH2" Residue "B GLU 698": "OE1" <-> "OE2" Residue "B TYR 702": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 707": "OD1" <-> "OD2" Residue "B GLU 716": "OE1" <-> "OE2" Residue "B ARG 722": "NH1" <-> "NH2" Residue "B GLU 772": "OE1" <-> "OE2" Residue "B GLU 815": "OE1" <-> "OE2" Residue "B GLU 836": "OE1" <-> "OE2" Residue "B GLU 847": "OE1" <-> "OE2" Residue "B GLU 864": "OE1" <-> "OE2" Residue "B GLU 873": "OE1" <-> "OE2" Residue "B TYR 884": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 902": "OE1" <-> "OE2" Residue "B GLU 903": "OE1" <-> "OE2" Residue "B ARG 950": "NH1" <-> "NH2" Residue "B ASP 986": "OD1" <-> "OD2" Residue "B GLU 992": "OE1" <-> "OE2" Residue "B GLU 1015": "OE1" <-> "OE2" Residue "B GLU 1017": "OE1" <-> "OE2" Residue "B PHE 1027": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 13": "OD1" <-> "OD2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 49": "OE1" <-> "OE2" Residue "C PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "C ARG 135": "NH1" <-> "NH2" Residue "C TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 162": "OE1" <-> "OE2" 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: 6592 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1345 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 4, 'TRANS': 163} Chain: "B" Number of atoms: 3877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 467, 3877 Classifications: {'peptide': 467} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 434} Chain breaks: 2 Chain: "C" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1370 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'peptide': 168, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 163, None: 2} Not linked: pdbres="GLU C 168 " pdbres="GNP C 201 " Not linked: pdbres="GNP C 201 " pdbres=" MG C 202 " Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 4.25, per 1000 atoms: 0.64 Number of scatterers: 6592 At special positions: 0 Unit cell: (73.485, 100.11, 124.605, 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 27 16.00 P 3 15.00 Mg 1 11.99 O 1251 8.00 N 1134 7.00 C 4176 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: 2.54 Conformation dependent library (CDL) restraints added in 1.4 seconds 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1538 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 5 sheets defined 50.7% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 16 through 24 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 61 through 63 No H-bonds generated for 'chain 'A' and resid 61 through 63' Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.710A pdb=" N ARG A 68 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 69 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N MET A 72 " --> pdb=" O ASP A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 91 No H-bonds generated for 'chain 'A' and resid 88 through 91' Processing helix chain 'A' and resid 93 through 104 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 152 through 167 Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 606 through 613 Processing helix chain 'B' and resid 621 through 633 removed outlier: 3.824A pdb=" N ARG B 625 " --> pdb=" O PRO B 621 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N ARG B 632 " --> pdb=" O LEU B 628 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N SER B 633 " --> pdb=" O THR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 648 Processing helix chain 'B' and resid 657 through 665 Processing helix chain 'B' and resid 672 through 680 removed outlier: 3.700A pdb=" N ARG B 676 " --> pdb=" O ALA B 672 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 679 " --> pdb=" O LYS B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 698 removed outlier: 3.550A pdb=" N LEU B 690 " --> pdb=" O GLN B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 706 removed outlier: 3.557A pdb=" N GLU B 705 " --> pdb=" O TYR B 702 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 706 " --> pdb=" O ASP B 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 720 removed outlier: 3.694A pdb=" N GLN B 712 " --> pdb=" O ALA B 708 " (cutoff:3.500A) Processing helix chain 'B' and resid 729 through 742 removed outlier: 3.810A pdb=" N ILE B 742 " --> pdb=" O GLN B 738 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 773 No H-bonds generated for 'chain 'B' and resid 771 through 773' Processing helix chain 'B' and resid 781 through 797 Processing helix chain 'B' and resid 801 through 803 No H-bonds generated for 'chain 'B' and resid 801 through 803' Processing helix chain 'B' and resid 808 through 810 No H-bonds generated for 'chain 'B' and resid 808 through 810' Processing helix chain 'B' and resid 814 through 817 No H-bonds generated for 'chain 'B' and resid 814 through 817' Processing helix chain 'B' and resid 819 through 841 Processing helix chain 'B' and resid 845 through 864 Processing helix chain 'B' and resid 868 through 878 removed outlier: 3.735A pdb=" N SER B 876 " --> pdb=" O LEU B 872 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA B 877 " --> pdb=" O GLU B 873 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 884 No H-bonds generated for 'chain 'B' and resid 881 through 884' Processing helix chain 'B' and resid 887 through 891 removed outlier: 3.570A pdb=" N GLU B 891 " --> pdb=" O ASP B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 887 through 891' Processing helix chain 'B' and resid 895 through 919 removed outlier: 3.839A pdb=" N LEU B 907 " --> pdb=" O GLU B 903 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER B 908 " --> pdb=" O ALA B 904 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLU B 909 " --> pdb=" O HIS B 905 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASP B 910 " --> pdb=" O GLU B 906 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N HIS B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N TYR B 912 " --> pdb=" O SER B 908 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS B 913 " --> pdb=" O GLU B 909 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS B 914 " --> pdb=" O ASP B 910 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR B 915 " --> pdb=" O HIS B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 930 through 943 removed outlier: 3.630A pdb=" N LYS B 939 " --> pdb=" O THR B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 958 through 975 removed outlier: 3.811A pdb=" N GLN B 972 " --> pdb=" O THR B 968 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLN B 973 " --> pdb=" O GLY B 969 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N TYR B 974 " --> pdb=" O GLU B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 992 Processing helix chain 'B' and resid 1002 through 1016 Processing helix chain 'C' and resid 16 through 24 Processing helix chain 'C' and resid 67 through 74 removed outlier: 3.902A pdb=" N MET C 72 " --> pdb=" O ASP C 69 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG C 73 " --> pdb=" O GLN C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 104 removed outlier: 3.516A pdb=" N GLU C 91 " --> pdb=" O THR C 87 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 93 " --> pdb=" O SER C 89 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N HIS C 94 " --> pdb=" O PHE C 90 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N HIS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 137 Processing helix chain 'C' and resid 152 through 167 removed outlier: 3.581A pdb=" N PHE C 156 " --> pdb=" O VAL C 152 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR C 157 " --> pdb=" O ASP C 153 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 140 through 143 removed outlier: 6.802A pdb=" N PHE A 78 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N VAL A 114 " --> pdb=" O PHE A 78 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N CYS A 80 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N ASN A 116 " --> pdb=" O CYS A 80 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N PHE A 82 " --> pdb=" O ASN A 116 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N TYR A 4 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LEU A 52 " --> pdb=" O TYR A 4 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU A 6 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ASP A 54 " --> pdb=" O LEU A 6 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL A 8 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU A 56 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N GLY A 10 " --> pdb=" O LEU A 56 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 947 through 950 Processing sheet with id= C, first strand: chain 'B' and resid 586 through 589 removed outlier: 5.450A pdb=" N GLU B 589 " --> pdb=" O ILE B 601 " (cutoff:3.500A) removed outlier: 6.010A pdb=" N ILE B 601 " --> pdb=" O GLU B 589 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 2 through 4 removed outlier: 4.090A pdb=" N THR C 2 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 77 through 83 removed outlier: 7.516A pdb=" N CYS C 80 " --> pdb=" O PRO C 110 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL C 112 " --> pdb=" O CYS C 80 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N PHE C 82 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL C 114 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 8.048A pdb=" N GLY C 115 " --> pdb=" O PRO C 140 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N ILE C 142 " --> pdb=" O GLY C 115 " (cutoff:3.500A) No H-bonds generated for sheet with id= E 259 hydrogen bonds defined for protein. 738 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: 1.80 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1862 1.33 - 1.45: 1020 1.45 - 1.57: 3799 1.57 - 1.68: 3 1.68 - 1.80: 44 Bond restraints: 6728 Sorted by residual: bond pdb=" N3B GNP C 201 " pdb=" PG GNP C 201 " ideal model delta sigma weight residual 1.801 1.689 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" O5' GNP C 201 " pdb=" PA GNP C 201 " ideal model delta sigma weight residual 1.660 1.548 0.112 2.00e-02 2.50e+03 3.12e+01 bond pdb=" N3B GNP C 201 " pdb=" PB GNP C 201 " ideal model delta sigma weight residual 1.681 1.621 0.060 2.00e-02 2.50e+03 9.10e+00 bond pdb=" O3A GNP C 201 " pdb=" PB GNP C 201 " ideal model delta sigma weight residual 1.687 1.631 0.056 2.00e-02 2.50e+03 7.72e+00 bond pdb=" N ILE C 163 " pdb=" CA ILE C 163 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.65e+00 ... (remaining 6723 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.41: 141 105.41 - 112.61: 3569 112.61 - 119.80: 2323 119.80 - 127.00: 2993 127.00 - 134.20: 75 Bond angle restraints: 9101 Sorted by residual: angle pdb=" N3B GNP C 201 " pdb=" PB GNP C 201 " pdb=" O3A GNP C 201 " ideal model delta sigma weight residual 100.48 111.12 -10.64 3.00e+00 1.11e-01 1.26e+01 angle pdb=" PB GNP C 201 " pdb=" N3B GNP C 201 " pdb=" PG GNP C 201 " ideal model delta sigma weight residual 123.35 113.90 9.45 3.00e+00 1.11e-01 9.92e+00 angle pdb=" O1B GNP C 201 " pdb=" PB GNP C 201 " pdb=" O2B GNP C 201 " ideal model delta sigma weight residual 119.66 110.34 9.32 3.00e+00 1.11e-01 9.66e+00 angle pdb=" CA LEU A 23 " pdb=" CB LEU A 23 " pdb=" CG LEU A 23 " ideal model delta sigma weight residual 116.30 105.54 10.76 3.50e+00 8.16e-02 9.45e+00 angle pdb=" N PRO B 925 " pdb=" CA PRO B 925 " pdb=" C PRO B 925 " ideal model delta sigma weight residual 112.47 106.25 6.22 2.06e+00 2.36e-01 9.12e+00 ... (remaining 9096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.90: 3674 15.90 - 31.80: 362 31.80 - 47.69: 76 47.69 - 63.59: 18 63.59 - 79.49: 9 Dihedral angle restraints: 4139 sinusoidal: 1770 harmonic: 2369 Sorted by residual: dihedral pdb=" CA PRO B 924 " pdb=" C PRO B 924 " pdb=" N PRO B 925 " pdb=" CA PRO B 925 " ideal model delta harmonic sigma weight residual 180.00 113.20 66.80 0 5.00e+00 4.00e-02 1.78e+02 dihedral pdb=" CA CYS B 926 " pdb=" C CYS B 926 " pdb=" N VAL B 927 " pdb=" CA VAL B 927 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA ASN B 923 " pdb=" C ASN B 923 " pdb=" N PRO B 924 " pdb=" CA PRO B 924 " ideal model delta harmonic sigma weight residual -180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 490 0.039 - 0.077: 376 0.077 - 0.116: 116 0.116 - 0.154: 18 0.154 - 0.193: 4 Chirality restraints: 1004 Sorted by residual: chirality pdb=" C2' GNP C 201 " pdb=" C1' GNP C 201 " pdb=" C3' GNP C 201 " pdb=" O2' GNP C 201 " both_signs ideal model delta sigma weight residual False -2.55 -2.74 0.19 2.00e-01 2.50e+01 9.31e-01 chirality pdb=" CA ILE C 163 " pdb=" N ILE C 163 " pdb=" C ILE C 163 " pdb=" CB ILE C 163 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.46e-01 chirality pdb=" CB VAL B 840 " pdb=" CA VAL B 840 " pdb=" CG1 VAL B 840 " pdb=" CG2 VAL B 840 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.96e-01 ... (remaining 1001 not shown) Planarity restraints: 1176 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 924 " -0.062 5.00e-02 4.00e+02 9.23e-02 1.36e+01 pdb=" N PRO B 925 " 0.160 5.00e-02 4.00e+02 pdb=" CA PRO B 925 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 925 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 930 " -0.019 2.00e-02 2.50e+03 1.50e-02 3.95e+00 pdb=" CG PHE B 930 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE B 930 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 930 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 930 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 930 " -0.008 2.00e-02 2.50e+03 pdb=" CZ PHE B 930 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN B 923 " -0.028 5.00e-02 4.00e+02 4.25e-02 2.88e+00 pdb=" N PRO B 924 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 924 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 924 " -0.023 5.00e-02 4.00e+02 ... (remaining 1173 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 28 2.50 - 3.10: 4852 3.10 - 3.70: 9863 3.70 - 4.30: 14813 4.30 - 4.90: 24698 Nonbonded interactions: 54254 Sorted by model distance: nonbonded pdb=" OG SER C 17 " pdb="MG MG C 202 " model vdw 1.897 2.170 nonbonded pdb=" OG1 THR C 35 " pdb="MG MG C 202 " model vdw 1.994 2.170 nonbonded pdb=" O1G GNP C 201 " pdb="MG MG C 202 " model vdw 2.123 2.170 nonbonded pdb=" OE2 GLU B 783 " pdb=" NE2 GLN B 787 " model vdw 2.188 2.520 nonbonded pdb=" O VAL C 8 " pdb=" OG1 THR C 58 " model vdw 2.223 2.440 ... (remaining 54249 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 1 through 30 or (resid 31 and (name N or name CA or name C \ or name O or name CB )) or resid 32 through 167 or (resid 168 and (name N or na \ me CA or name C or name O or name CB )))) selection = (chain 'C' and resid 1 through 168) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.320 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: 0.000 Extract box with map and model: 1.810 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.840 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 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 : 0.012 0.112 6728 Z= 0.766 Angle : 0.805 10.759 9101 Z= 0.430 Chirality : 0.053 0.193 1004 Planarity : 0.005 0.092 1176 Dihedral : 13.579 79.491 2601 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: -1.10 (0.28), residues: 793 helix: -1.10 (0.25), residues: 390 sheet: -0.69 (0.52), residues: 85 loop : 0.10 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 729 HIS 0.005 0.001 HIS B 888 PHE 0.034 0.002 PHE B 930 TYR 0.014 0.002 TYR B 615 ARG 0.009 0.001 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 111 MET cc_start: 0.6418 (ttm) cc_final: 0.5883 (ttm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.2019 time to fit residues: 14.4858 Evaluate side-chains 24 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 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 61 GLN B 566 GLN ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6728 Z= 0.157 Angle : 0.501 7.434 9101 Z= 0.261 Chirality : 0.040 0.174 1004 Planarity : 0.004 0.076 1176 Dihedral : 5.172 57.907 915 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.55 % Allowed : 5.05 % Favored : 94.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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 (0.29), residues: 793 helix: 0.60 (0.26), residues: 384 sheet: -0.62 (0.50), residues: 88 loop : 0.49 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 729 HIS 0.002 0.001 HIS C 166 PHE 0.019 0.001 PHE B 588 TYR 0.025 0.001 TYR A 157 ARG 0.003 0.000 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 28 time to evaluate : 0.846 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 30 average time/residue: 0.2367 time to fit residues: 10.4876 Evaluate side-chains 23 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6728 Z= 0.149 Angle : 0.468 9.611 9101 Z= 0.236 Chirality : 0.039 0.142 1004 Planarity : 0.004 0.075 1176 Dihedral : 4.748 57.728 915 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.55 % Allowed : 6.15 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 1.07 (0.30), residues: 793 helix: 1.18 (0.26), residues: 395 sheet: -0.21 (0.50), residues: 88 loop : 0.59 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 729 HIS 0.002 0.000 HIS B 616 PHE 0.011 0.001 PHE B 588 TYR 0.017 0.001 TYR A 157 ARG 0.003 0.000 ARG B1026 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.813 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 27 average time/residue: 0.1475 time to fit residues: 6.6242 Evaluate side-chains 22 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 606 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 68 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 61 GLN ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6728 Z= 0.293 Angle : 0.511 7.989 9101 Z= 0.258 Chirality : 0.039 0.130 1004 Planarity : 0.004 0.080 1176 Dihedral : 4.769 59.876 915 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.23 % Allowed : 6.56 % Favored : 92.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 1.65 (0.30), residues: 793 helix: 1.71 (0.26), residues: 395 sheet: -0.10 (0.49), residues: 88 loop : 0.86 (0.37), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 729 HIS 0.003 0.001 HIS B 764 PHE 0.010 0.001 PHE B 577 TYR 0.011 0.001 TYR A 157 ARG 0.003 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 20 time to evaluate : 1.710 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 27 average time/residue: 0.1645 time to fit residues: 7.7680 Evaluate side-chains 23 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain C residue 67 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 68 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 15 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6728 Z= 0.139 Angle : 0.439 8.524 9101 Z= 0.220 Chirality : 0.038 0.132 1004 Planarity : 0.003 0.076 1176 Dihedral : 4.590 57.367 915 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.68 % Allowed : 7.92 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 1.88 (0.30), residues: 793 helix: 1.95 (0.26), residues: 392 sheet: 0.06 (0.50), residues: 88 loop : 0.87 (0.37), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 809 HIS 0.001 0.000 HIS A 95 PHE 0.008 0.001 PHE B 577 TYR 0.007 0.001 TYR A 157 ARG 0.002 0.000 ARG B1026 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 21 time to evaluate : 0.769 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 25 average time/residue: 0.1891 time to fit residues: 7.3053 Evaluate side-chains 24 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 chunk 25 optimal weight: 40.0000 chunk 40 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.002 0.037 6728 Z= 0.137 Angle : 0.440 9.841 9101 Z= 0.218 Chirality : 0.038 0.131 1004 Planarity : 0.003 0.074 1176 Dihedral : 4.449 56.325 915 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.82 % Allowed : 8.33 % Favored : 90.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.05 (0.30), residues: 793 helix: 2.09 (0.26), residues: 389 sheet: 0.23 (0.50), residues: 88 loop : 0.94 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 809 HIS 0.001 0.000 HIS A 95 PHE 0.008 0.001 PHE B 577 TYR 0.006 0.001 TYR B 796 ARG 0.002 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.911 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.1755 time to fit residues: 7.2168 Evaluate side-chains 24 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 755 GLN ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6728 Z= 0.139 Angle : 0.432 9.099 9101 Z= 0.216 Chirality : 0.038 0.130 1004 Planarity : 0.003 0.074 1176 Dihedral : 4.388 55.760 915 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.82 % Allowed : 8.20 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.16 (0.30), residues: 793 helix: 2.17 (0.26), residues: 389 sheet: 0.36 (0.50), residues: 88 loop : 0.99 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 809 HIS 0.001 0.000 HIS B 616 PHE 0.008 0.001 PHE B 577 TYR 0.006 0.001 TYR B 796 ARG 0.003 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 21 time to evaluate : 0.821 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 25 average time/residue: 0.1536 time to fit residues: 6.4679 Evaluate side-chains 24 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 20 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 chunk 51 optimal weight: 0.0770 chunk 37 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 66 optimal weight: 0.0670 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.3312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6728 Z= 0.122 Angle : 0.437 11.700 9101 Z= 0.215 Chirality : 0.038 0.130 1004 Planarity : 0.003 0.069 1176 Dihedral : 4.285 54.529 915 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.82 % Allowed : 8.20 % Favored : 90.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.25 (0.30), residues: 793 helix: 2.27 (0.26), residues: 388 sheet: 0.47 (0.51), residues: 88 loop : 0.97 (0.38), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 809 HIS 0.002 0.000 HIS B 616 PHE 0.007 0.001 PHE B 577 TYR 0.015 0.001 TYR A 157 ARG 0.003 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 23 time to evaluate : 0.818 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 27 average time/residue: 0.1557 time to fit residues: 6.9469 Evaluate side-chains 25 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 75 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6728 Z= 0.135 Angle : 0.459 11.676 9101 Z= 0.221 Chirality : 0.038 0.130 1004 Planarity : 0.003 0.069 1176 Dihedral : 4.252 54.321 915 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.82 % Allowed : 8.47 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.37 (0.30), residues: 793 helix: 2.35 (0.26), residues: 390 sheet: 0.59 (0.51), residues: 88 loop : 1.02 (0.38), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 809 HIS 0.008 0.000 HIS B 616 PHE 0.007 0.001 PHE B 577 TYR 0.007 0.001 TYR B 796 ARG 0.002 0.000 ARG C 135 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.876 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 24 average time/residue: 0.1328 time to fit residues: 5.3896 Evaluate side-chains 25 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 62 optimal weight: 10.0000 chunk 6 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 0.0270 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6728 Z= 0.166 Angle : 0.474 12.076 9101 Z= 0.230 Chirality : 0.038 0.163 1004 Planarity : 0.003 0.070 1176 Dihedral : 4.311 55.393 915 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.82 % Allowed : 8.47 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.44 (0.31), residues: 793 helix: 2.37 (0.26), residues: 393 sheet: 0.63 (0.52), residues: 88 loop : 1.09 (0.38), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 729 HIS 0.009 0.001 HIS B 616 PHE 0.008 0.001 PHE B 577 TYR 0.018 0.001 TYR B 615 ARG 0.003 0.000 ARG B 612 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1586 Ramachandran restraints generated. 793 Oldfield, 0 Emsley, 793 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.817 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 24 average time/residue: 0.1512 time to fit residues: 6.1176 Evaluate side-chains 25 residues out of total 734 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 831 LEU Chi-restraints excluded: chain C residue 67 MET Chi-restraints excluded: chain C residue 152 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.0870 chunk 62 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 45 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 overall best weight: 3.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 764 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.031726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2337 r_free = 0.2337 target = 0.023706 restraints weight = 38926.711| |-----------------------------------------------------------------------------| r_work (start): 0.2348 rms_B_bonded: 4.68 r_work (final): 0.2348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6728 Z= 0.292 Angle : 0.531 12.186 9101 Z= 0.262 Chirality : 0.039 0.125 1004 Planarity : 0.004 0.073 1176 Dihedral : 4.718 58.675 915 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.68 % Allowed : 8.61 % Favored : 90.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 2.30 (0.31), residues: 793 helix: 2.20 (0.26), residues: 397 sheet: 0.36 (0.50), residues: 91 loop : 1.18 (0.39), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 729 HIS 0.005 0.001 HIS B 616 PHE 0.010 0.001 PHE B 577 TYR 0.026 0.001 TYR B 615 ARG 0.004 0.000 ARG B 612 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1377.95 seconds wall clock time: 26 minutes 10.39 seconds (1570.39 seconds total)