Starting phenix.real_space_refine on Sat Mar 16 07:01:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smz_40607/03_2024/8smz_40607.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smz_40607/03_2024/8smz_40607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smz_40607/03_2024/8smz_40607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smz_40607/03_2024/8smz_40607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smz_40607/03_2024/8smz_40607.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8smz_40607/03_2024/8smz_40607.pdb" } resolution = 3.2 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= 0.105 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 Zn 2 6.06 5 P 294 5.49 5 S 32 5.16 5 C 7891 2.51 5 N 2608 2.21 5 O 3171 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 72": "OD1" <-> "OD2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 72": "OD1" <-> "OD2" Residue "L PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" 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: 13998 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 34.493 67.206 42.369 1.00 54.60 S ATOM 12446 SG CYS K 51 32.878 63.788 42.788 1.00 53.45 S ATOM 12470 SG CYS K 54 34.673 64.732 39.472 1.00 59.59 S ATOM 12187 SG CYS K 16 22.650 64.083 47.853 1.00 61.09 S ATOM 12205 SG CYS K 19 20.144 62.240 49.932 1.00 66.08 S ATOM 12335 SG CYS K 36 22.147 65.128 51.321 1.00 55.44 S ATOM 12357 SG CYS K 39 23.894 61.698 50.708 1.00 56.03 S Time building chain proxies: 8.18, per 1000 atoms: 0.58 Number of scatterers: 13998 At special positions: 0 Unit cell: (108.896, 128.816, 127.488, 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) Zn 2 29.99 S 32 16.00 P 294 15.00 O 3171 8.00 N 2608 7.00 C 7891 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: 6.90 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " Number of angles added : 9 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1888 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 11 sheets defined 64.8% alpha, 4.2% beta 136 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 5.72 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.502A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.714A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.588A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.967A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.906A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.597A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.560A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.608A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.545A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.795A pdb=" N GLN D 47 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.564A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.563A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.894A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER D 112 " --> pdb=" O LYS D 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.508A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.512A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.863A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.526A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.610A pdb=" N VAL G 30 " --> pdb=" O PRO G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.625A pdb=" N ALA G 86 " --> pdb=" O HIS G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.541A pdb=" N MET H 59 " --> pdb=" O SER H 55 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.592A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 4.088A pdb=" N THR K 62 " --> pdb=" O VAL K 58 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 removed outlier: 3.899A pdb=" N ILE K 79 " --> pdb=" O GLU K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.961A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LYS K 89 " --> pdb=" O PRO K 85 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 4.444A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARG L 125 " --> pdb=" O PRO L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 146 removed outlier: 3.728A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.952A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.328A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.767A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.302A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.899A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24 461 hydrogen bonds defined for protein. 1365 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 349 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 136 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.92 Time building geometry restraints manager: 7.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3294 1.34 - 1.46: 4482 1.46 - 1.58: 6455 1.58 - 1.70: 586 1.70 - 1.82: 47 Bond restraints: 14864 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.76e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.27e+00 bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.12e+00 bond pdb=" CB MET B 84 " pdb=" CG MET B 84 " ideal model delta sigma weight residual 1.520 1.489 0.031 3.00e-02 1.11e+03 1.10e+00 bond pdb=" CG PRO L 61 " pdb=" CD PRO L 61 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.70e-02 1.37e+03 1.02e+00 ... (remaining 14859 not shown) Histogram of bond angle deviations from ideal: 98.57 - 105.66: 1570 105.66 - 112.75: 8231 112.75 - 119.84: 5098 119.84 - 126.93: 5681 126.93 - 134.02: 773 Bond angle restraints: 21353 Sorted by residual: angle pdb=" C ASN L 7 " pdb=" N LYS L 8 " pdb=" CA LYS L 8 " ideal model delta sigma weight residual 120.44 117.21 3.23 1.30e+00 5.92e-01 6.17e+00 angle pdb=" N GLY H 104 " pdb=" CA GLY H 104 " pdb=" C GLY H 104 " ideal model delta sigma weight residual 113.18 118.89 -5.71 2.37e+00 1.78e-01 5.81e+00 angle pdb=" CB LYS L 8 " pdb=" CG LYS L 8 " pdb=" CD LYS L 8 " ideal model delta sigma weight residual 111.30 116.82 -5.52 2.30e+00 1.89e-01 5.76e+00 angle pdb=" CB LEU L 86 " pdb=" CG LEU L 86 " pdb=" CD2 LEU L 86 " ideal model delta sigma weight residual 110.70 103.86 6.84 3.00e+00 1.11e-01 5.20e+00 angle pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " pdb=" C1' DA J -73 " ideal model delta sigma weight residual 101.60 104.69 -3.09 1.50e+00 4.44e-01 4.23e+00 ... (remaining 21348 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.50: 6742 34.50 - 69.00: 1456 69.00 - 103.50: 24 103.50 - 138.00: 0 138.00 - 172.50: 2 Dihedral angle restraints: 8224 sinusoidal: 5302 harmonic: 2922 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 47.50 172.50 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 68.78 151.22 1 3.50e+01 8.16e-04 1.47e+01 dihedral pdb=" CA ILE L 78 " pdb=" C ILE L 78 " pdb=" N ASN L 79 " pdb=" CA ASN L 79 " ideal model delta harmonic sigma weight residual 180.00 162.83 17.17 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 8221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1868 0.042 - 0.083: 463 0.083 - 0.125: 79 0.125 - 0.167: 7 0.167 - 0.208: 2 Chirality restraints: 2419 Sorted by residual: chirality pdb=" CG LEU L 86 " pdb=" CB LEU L 86 " pdb=" CD1 LEU L 86 " pdb=" CD2 LEU L 86 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE L 123 " pdb=" CA ILE L 123 " pdb=" CG1 ILE L 123 " pdb=" CG2 ILE L 123 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" CA ILE L 84 " pdb=" N ILE L 84 " pdb=" C ILE L 84 " pdb=" CB ILE L 84 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.83e-01 ... (remaining 2416 not shown) Planarity restraints: 1688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS L 75 " -0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO L 76 " 0.087 5.00e-02 4.00e+02 pdb=" CA PRO L 76 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 76 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.028 2.00e-02 2.50e+03 1.15e-02 3.97e+00 pdb=" N9 DG I 47 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.027 2.00e-02 2.50e+03 1.17e-02 3.78e+00 pdb=" N9 DA I -35 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.002 2.00e-02 2.50e+03 ... (remaining 1685 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1800 2.76 - 3.47: 17296 3.47 - 4.19: 37748 4.19 - 4.90: 58950 Nonbonded interactions: 115796 Sorted by model distance: nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.330 3.350 nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.330 3.350 nonbonded pdb=" N4 DC I 21 " pdb=" O6 DG J -21 " model vdw 2.227 2.520 nonbonded pdb=" N SER C 11 " pdb=" O SER D 123 " model vdw 2.249 2.520 nonbonded pdb=" N SER G 11 " pdb=" O SER H 123 " model vdw 2.254 2.520 ... (remaining 115791 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.17 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.420 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 46.370 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.004 0.040 14864 Z= 0.215 Angle : 0.572 6.842 21353 Z= 0.339 Chirality : 0.037 0.208 2419 Planarity : 0.005 0.050 1688 Dihedral : 26.569 172.502 6336 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.15 (0.27), residues: 983 helix: 1.95 (0.21), residues: 621 sheet: -0.29 (0.99), residues: 23 loop : -1.48 (0.30), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP L 141 HIS 0.003 0.001 HIS H 49 PHE 0.012 0.002 PHE L 69 TYR 0.014 0.001 TYR G 50 ARG 0.007 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.263 Fit side-chains REVERT: A 77 ASP cc_start: 0.7661 (t0) cc_final: 0.7141 (t0) REVERT: C 36 LYS cc_start: 0.8450 (mttm) cc_final: 0.8169 (mmmm) outliers start: 0 outliers final: 0 residues processed: 112 average time/residue: 0.3667 time to fit residues: 54.7039 Evaluate side-chains 96 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 110 optimal weight: 30.0000 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14864 Z= 0.252 Angle : 0.562 7.540 21353 Z= 0.331 Chirality : 0.036 0.146 2419 Planarity : 0.004 0.045 1688 Dihedral : 29.486 172.805 4332 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.70 % Allowed : 4.91 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.40 (0.27), residues: 983 helix: 2.16 (0.21), residues: 623 sheet: -0.02 (1.02), residues: 23 loop : -1.47 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 141 HIS 0.004 0.001 HIS H 49 PHE 0.009 0.001 PHE A 78 TYR 0.014 0.001 TYR D 121 ARG 0.005 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7718 (t0) cc_final: 0.7253 (t0) REVERT: B 79 LYS cc_start: 0.8451 (mttm) cc_final: 0.8159 (mttt) outliers start: 6 outliers final: 3 residues processed: 104 average time/residue: 0.3752 time to fit residues: 51.9255 Evaluate side-chains 96 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 93 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain L residue 84 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 110 optimal weight: 20.0000 chunk 119 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 50.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14864 Z= 0.377 Angle : 0.605 6.834 21353 Z= 0.353 Chirality : 0.039 0.151 2419 Planarity : 0.005 0.046 1688 Dihedral : 29.681 171.836 4332 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.29 % Allowed : 7.71 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.08 (0.27), residues: 983 helix: 1.93 (0.21), residues: 623 sheet: 0.00 (0.99), residues: 23 loop : -1.64 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 141 HIS 0.010 0.002 HIS L 75 PHE 0.015 0.002 PHE A 78 TYR 0.014 0.002 TYR D 121 ARG 0.005 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.178 Fit side-chains REVERT: A 77 ASP cc_start: 0.7821 (t0) cc_final: 0.7288 (t0) REVERT: B 79 LYS cc_start: 0.8526 (mttm) cc_final: 0.8164 (mttt) outliers start: 11 outliers final: 8 residues processed: 96 average time/residue: 0.3748 time to fit residues: 47.8147 Evaluate side-chains 96 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 84 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14864 Z= 0.199 Angle : 0.556 6.767 21353 Z= 0.331 Chirality : 0.036 0.183 2419 Planarity : 0.004 0.044 1688 Dihedral : 29.586 172.566 4332 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.93 % Allowed : 8.06 % Favored : 91.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.46 (0.27), residues: 983 helix: 2.24 (0.21), residues: 624 sheet: 0.03 (0.99), residues: 23 loop : -1.53 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 77 HIS 0.003 0.001 HIS A 39 PHE 0.009 0.001 PHE F 61 TYR 0.012 0.001 TYR D 121 ARG 0.002 0.000 ARG L 125 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 94 time to evaluate : 1.138 Fit side-chains REVERT: A 77 ASP cc_start: 0.7744 (t0) cc_final: 0.7281 (t0) outliers start: 8 outliers final: 7 residues processed: 99 average time/residue: 0.3632 time to fit residues: 47.9984 Evaluate side-chains 99 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 84 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 100 optimal weight: 10.0000 chunk 81 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 105 optimal weight: 8.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.0745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14864 Z= 0.231 Angle : 0.546 5.707 21353 Z= 0.323 Chirality : 0.036 0.143 2419 Planarity : 0.004 0.041 1688 Dihedral : 29.491 173.250 4332 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.17 % Allowed : 8.88 % Favored : 89.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.53 (0.27), residues: 983 helix: 2.30 (0.21), residues: 624 sheet: 0.02 (0.97), residues: 23 loop : -1.52 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 33 HIS 0.004 0.001 HIS H 49 PHE 0.010 0.001 PHE E 67 TYR 0.011 0.001 TYR D 121 ARG 0.004 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 1.074 Fit side-chains REVERT: A 77 ASP cc_start: 0.7812 (t0) cc_final: 0.7358 (t0) REVERT: B 79 LYS cc_start: 0.8500 (mttm) cc_final: 0.8151 (mttt) outliers start: 10 outliers final: 9 residues processed: 99 average time/residue: 0.3836 time to fit residues: 50.6086 Evaluate side-chains 100 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 91 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.0010 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14864 Z= 0.187 Angle : 0.534 6.597 21353 Z= 0.318 Chirality : 0.035 0.127 2419 Planarity : 0.004 0.040 1688 Dihedral : 29.452 173.247 4332 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.17 % Allowed : 9.81 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.65 (0.27), residues: 983 helix: 2.41 (0.21), residues: 623 sheet: 0.10 (0.98), residues: 23 loop : -1.48 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 PHE 0.008 0.001 PHE E 67 TYR 0.010 0.001 TYR D 121 ARG 0.004 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.008 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7797 (t0) cc_final: 0.7378 (t0) outliers start: 10 outliers final: 10 residues processed: 94 average time/residue: 0.3713 time to fit residues: 46.6902 Evaluate side-chains 99 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14864 Z= 0.201 Angle : 0.531 6.417 21353 Z= 0.316 Chirality : 0.035 0.128 2419 Planarity : 0.004 0.038 1688 Dihedral : 29.401 173.798 4332 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.40 % Allowed : 9.81 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.71 (0.27), residues: 983 helix: 2.47 (0.21), residues: 622 sheet: 0.13 (0.99), residues: 23 loop : -1.47 (0.30), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 33 HIS 0.004 0.001 HIS K 65 PHE 0.008 0.001 PHE F 61 TYR 0.011 0.001 TYR D 121 ARG 0.004 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 92 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7823 (t0) cc_final: 0.7406 (t0) REVERT: B 79 LYS cc_start: 0.8488 (mttm) cc_final: 0.8137 (mttt) REVERT: L 3 LEU cc_start: 0.6240 (tp) cc_final: 0.6036 (tp) outliers start: 12 outliers final: 11 residues processed: 99 average time/residue: 0.3607 time to fit residues: 48.0165 Evaluate side-chains 101 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 86 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.4980 chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14864 Z= 0.166 Angle : 0.523 6.833 21353 Z= 0.312 Chirality : 0.034 0.124 2419 Planarity : 0.004 0.038 1688 Dihedral : 29.368 173.407 4332 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.29 % Allowed : 10.05 % Favored : 88.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.79 (0.27), residues: 983 helix: 2.53 (0.21), residues: 623 sheet: 0.15 (1.00), residues: 23 loop : -1.45 (0.30), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 33 HIS 0.003 0.001 HIS A 39 PHE 0.008 0.001 PHE E 67 TYR 0.009 0.001 TYR D 121 ARG 0.003 0.000 ARG G 99 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 90 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: A 77 ASP cc_start: 0.7795 (t0) cc_final: 0.7401 (t0) REVERT: L 3 LEU cc_start: 0.6232 (tp) cc_final: 0.6025 (tp) outliers start: 11 outliers final: 10 residues processed: 97 average time/residue: 0.3581 time to fit residues: 46.6260 Evaluate side-chains 101 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 109 optimal weight: 0.3980 chunk 65 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 115 optimal weight: 20.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 65 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14864 Z= 0.277 Angle : 0.553 6.248 21353 Z= 0.327 Chirality : 0.036 0.131 2419 Planarity : 0.004 0.039 1688 Dihedral : 29.474 172.334 4332 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.40 % Allowed : 10.05 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.58 (0.27), residues: 983 helix: 2.36 (0.21), residues: 624 sheet: 0.08 (0.99), residues: 23 loop : -1.53 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 33 HIS 0.005 0.001 HIS H 49 PHE 0.012 0.002 PHE A 78 TYR 0.012 0.001 TYR D 121 ARG 0.004 0.000 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.228 Fit side-chains REVERT: A 77 ASP cc_start: 0.7892 (t0) cc_final: 0.7432 (t0) REVERT: B 79 LYS cc_start: 0.8486 (mttm) cc_final: 0.8136 (mttt) REVERT: L 3 LEU cc_start: 0.6378 (tp) cc_final: 0.6175 (tp) outliers start: 12 outliers final: 12 residues processed: 101 average time/residue: 0.3596 time to fit residues: 48.4730 Evaluate side-chains 105 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 0.0030 chunk 54 optimal weight: 0.0980 chunk 80 optimal weight: 3.9990 chunk 121 optimal weight: 0.0060 chunk 111 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 overall best weight: 1.0208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN K 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14864 Z= 0.216 Angle : 0.544 6.311 21353 Z= 0.323 Chirality : 0.035 0.129 2419 Planarity : 0.004 0.039 1688 Dihedral : 29.470 172.352 4332 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.29 % Allowed : 10.40 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.61 (0.27), residues: 983 helix: 2.38 (0.21), residues: 624 sheet: 0.08 (0.99), residues: 23 loop : -1.52 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.004 0.001 HIS H 49 PHE 0.011 0.001 PHE A 78 TYR 0.011 0.001 TYR D 121 ARG 0.003 0.000 ARG H 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1966 Ramachandran restraints generated. 983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 1.088 Fit side-chains REVERT: A 77 ASP cc_start: 0.7868 (t0) cc_final: 0.7414 (t0) REVERT: B 79 LYS cc_start: 0.8479 (mttm) cc_final: 0.8127 (mttt) REVERT: L 3 LEU cc_start: 0.6248 (tp) cc_final: 0.6010 (tp) outliers start: 11 outliers final: 11 residues processed: 99 average time/residue: 0.3657 time to fit residues: 48.3532 Evaluate side-chains 103 residues out of total 850 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain K residue 35 LEU Chi-restraints excluded: chain L residue 49 VAL Chi-restraints excluded: chain L residue 84 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 4.9990 chunk 14 optimal weight: 0.0670 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN K 65 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.172194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.117666 restraints weight = 23141.704| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.66 r_work: 0.2944 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.0888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14864 Z= 0.182 Angle : 0.538 6.292 21353 Z= 0.320 Chirality : 0.035 0.129 2419 Planarity : 0.004 0.039 1688 Dihedral : 29.458 172.391 4332 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.40 % Allowed : 10.40 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.70 (0.27), residues: 983 helix: 2.46 (0.21), residues: 624 sheet: 0.09 (0.99), residues: 23 loop : -1.49 (0.30), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 61 HIS 0.003 0.001 HIS H 49 PHE 0.010 0.001 PHE E 67 TYR 0.010 0.001 TYR D 121 ARG 0.003 0.000 ARG H 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.67 seconds wall clock time: 43 minutes 2.65 seconds (2582.65 seconds total)