Starting phenix.real_space_refine on Sat Apr 6 20:24:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk3_27482/04_2024/8dk3_27482_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk3_27482/04_2024/8dk3_27482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk3_27482/04_2024/8dk3_27482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk3_27482/04_2024/8dk3_27482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk3_27482/04_2024/8dk3_27482_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk3_27482/04_2024/8dk3_27482_updated.pdb" } resolution = 3.28 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= 0.001 sd= 0.018 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 58 5.49 5 Mg 2 5.21 5 S 23 5.16 5 C 5414 2.51 5 N 1597 2.21 5 O 1811 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 8905 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 455, 3530 Classifications: {'peptide': 455} Link IDs: {'PTRANS': 12, 'TRANS': 442} Chain breaks: 2 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3494 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 12, 'TRANS': 437} Chain breaks: 2 Chain: "C" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 751 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "P" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 520 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "Q" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 546 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.51, per 1000 atoms: 0.51 Number of scatterers: 8905 At special positions: 0 Unit cell: (89.1, 111.1, 112.2, 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 23 16.00 P 58 15.00 Mg 2 11.99 O 1811 8.00 N 1597 7.00 C 5414 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: 4.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1834 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 40 helices and 8 sheets defined 40.5% alpha, 17.1% beta 26 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 49 through 59 removed outlier: 3.844A pdb=" N VAL A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 71 No H-bonds generated for 'chain 'A' and resid 69 through 71' Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 153 through 162 removed outlier: 3.609A pdb=" N ALA A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 174 removed outlier: 3.883A pdb=" N MET A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LYS A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP A 174 " --> pdb=" O GLN A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 195 Processing helix chain 'A' and resid 201 through 209 removed outlier: 3.731A pdb=" N ALA A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 223 Processing helix chain 'A' and resid 232 through 241 Processing helix chain 'A' and resid 857 through 882 removed outlier: 3.994A pdb=" N GLN A 882 " --> pdb=" O ASN A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 902 through 916 removed outlier: 3.945A pdb=" N ARG A 905 " --> pdb=" O GLU A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 932 through 943 Processing helix chain 'A' and resid 948 through 954 Processing helix chain 'A' and resid 956 through 958 No H-bonds generated for 'chain 'A' and resid 956 through 958' Processing helix chain 'A' and resid 986 through 1004 removed outlier: 4.410A pdb=" N GLU A 990 " --> pdb=" O GLY A 986 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A 991 " --> pdb=" O GLY A 987 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TYR A1003 " --> pdb=" O ALA A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1006 through 1009 Processing helix chain 'A' and resid 1029 through 1042 removed outlier: 3.735A pdb=" N GLY A1033 " --> pdb=" O HIS A1029 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A1034 " --> pdb=" O ALA A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1061 Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'B' and resid 49 through 59 removed outlier: 3.608A pdb=" N VAL B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B 56 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU B 59 " --> pdb=" O ALA B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 69 through 71 No H-bonds generated for 'chain 'B' and resid 69 through 71' Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.588A pdb=" N ARG B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 153 through 162 Processing helix chain 'B' and resid 165 through 171 removed outlier: 3.953A pdb=" N MET B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 Processing helix chain 'B' and resid 201 through 209 removed outlier: 3.759A pdb=" N ALA B 209 " --> pdb=" O LEU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 223 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 858 through 881 removed outlier: 3.733A pdb=" N ILE B 870 " --> pdb=" O GLU B 866 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLU B 871 " --> pdb=" O VAL B 867 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP B 876 " --> pdb=" O GLU B 872 " (cutoff:3.500A) Processing helix chain 'B' and resid 902 through 917 Processing helix chain 'B' and resid 931 through 943 Processing helix chain 'B' and resid 948 through 954 removed outlier: 4.047A pdb=" N LEU B 953 " --> pdb=" O GLY B 949 " (cutoff:3.500A) Processing helix chain 'B' and resid 956 through 959 Processing helix chain 'B' and resid 986 through 1004 removed outlier: 4.351A pdb=" N GLU B 990 " --> pdb=" O GLY B 986 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE B 991 " --> pdb=" O GLY B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1029 through 1042 removed outlier: 3.613A pdb=" N PHE B1042 " --> pdb=" O ALA B1038 " (cutoff:3.500A) Processing helix chain 'B' and resid 1055 through 1061 removed outlier: 3.941A pdb=" N HIS B1060 " --> pdb=" O ARG B1056 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N HIS B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 424 Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 446 through 456 Processing sheet with id= A, first strand: chain 'A' and resid 29 through 33 removed outlier: 7.297A pdb=" N THR A 113 " --> pdb=" O THR A 16 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE A 18 " --> pdb=" O ALA A 111 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ALA A 111 " --> pdb=" O ILE A 18 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU A 20 " --> pdb=" O ALA A 109 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA A 109 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 116 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A 119 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 140 " --> pdb=" O TRP A 128 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1074 through 1081 removed outlier: 3.780A pdb=" N GLU A1074 " --> pdb=" O ARG A1071 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 39 " --> pdb=" O ALA A1046 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ILE A1018 " --> pdb=" O VAL A1047 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N ILE A1049 " --> pdb=" O ILE A1018 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N LEU A1020 " --> pdb=" O ILE A1049 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 890 through 898 removed outlier: 4.160A pdb=" N GLU A 976 " --> pdb=" O VAL A 966 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP A 968 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU A 974 " --> pdb=" O ASP A 968 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 29 through 33 removed outlier: 7.006A pdb=" N THR B 113 " --> pdb=" O THR B 16 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE B 18 " --> pdb=" O ALA B 111 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ALA B 111 " --> pdb=" O ILE B 18 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N LEU B 20 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA B 109 " --> pdb=" O LEU B 20 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA B 125 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU B 144 " --> pdb=" O GLY B 124 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP B 128 " --> pdb=" O LYS B 140 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 39 through 42 removed outlier: 3.933A pdb=" N THR B 39 " --> pdb=" O ALA B1046 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 890 through 898 removed outlier: 3.847A pdb=" N GLU B 976 " --> pdb=" O VAL B 966 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP B 968 " --> pdb=" O LEU B 974 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 974 " --> pdb=" O ASP B 968 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 1065 through 1071 removed outlier: 4.067A pdb=" N ALA B1065 " --> pdb=" O LEU B1080 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 460 through 470 removed outlier: 3.610A pdb=" N TYR C 484 " --> pdb=" O LEU C 461 " (cutoff:3.500A) removed outlier: 8.695A pdb=" N GLU C 463 " --> pdb=" O LEU C 482 " (cutoff:3.500A) removed outlier: 11.215A pdb=" N LEU C 482 " --> pdb=" O GLU C 463 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ARG C 465 " --> pdb=" O PHE C 480 " (cutoff:3.500A) removed outlier: 10.824A pdb=" N PHE C 480 " --> pdb=" O ARG C 465 " (cutoff:3.500A) removed outlier: 9.716A pdb=" N PHE C 467 " --> pdb=" O TRP C 478 " (cutoff:3.500A) removed outlier: 11.043A pdb=" N TRP C 478 " --> pdb=" O PHE C 467 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 2.85 Time building geometry restraints manager: 4.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.36: 2961 1.36 - 1.50: 2895 1.50 - 1.65: 3283 1.65 - 1.80: 22 1.80 - 1.94: 16 Bond restraints: 9177 Sorted by residual: bond pdb=" N ASN B 63 " pdb=" CA ASN B 63 " ideal model delta sigma weight residual 1.464 1.454 0.010 9.80e-03 1.04e+04 9.60e-01 bond pdb=" CB VAL A 197 " pdb=" CG1 VAL A 197 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.73e-01 bond pdb=" CB VAL B1068 " pdb=" CG2 VAL B1068 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.55e-01 bond pdb=" CB THR B1062 " pdb=" CG2 THR B1062 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.54e-01 bond pdb=" CA THR B 88 " pdb=" CB THR B 88 " ideal model delta sigma weight residual 1.531 1.501 0.029 3.28e-02 9.30e+02 8.05e-01 ... (remaining 9172 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.09: 538 107.09 - 113.83: 5229 113.83 - 120.57: 3619 120.57 - 127.30: 3097 127.30 - 134.04: 162 Bond angle restraints: 12645 Sorted by residual: angle pdb=" C GLU C 475 " pdb=" CA GLU C 475 " pdb=" CB GLU C 475 " ideal model delta sigma weight residual 116.54 110.24 6.30 1.15e+00 7.56e-01 3.00e+01 angle pdb=" CA GLU C 475 " pdb=" C GLU C 475 " pdb=" N GLN C 476 " ideal model delta sigma weight residual 119.52 116.45 3.07 7.90e-01 1.60e+00 1.51e+01 angle pdb=" N GLY B1016 " pdb=" CA GLY B1016 " pdb=" C GLY B1016 " ideal model delta sigma weight residual 113.18 118.20 -5.02 2.37e+00 1.78e-01 4.49e+00 angle pdb=" N GLU C 475 " pdb=" CA GLU C 475 " pdb=" C GLU C 475 " ideal model delta sigma weight residual 108.31 111.46 -3.15 1.52e+00 4.33e-01 4.28e+00 angle pdb=" C ALA B 62 " pdb=" N ASN B 63 " pdb=" CA ASN B 63 " ideal model delta sigma weight residual 122.28 120.54 1.74 8.80e-01 1.29e+00 3.93e+00 ... (remaining 12640 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.79: 4886 22.79 - 45.58: 366 45.58 - 68.38: 135 68.38 - 91.17: 1 91.17 - 113.96: 1 Dihedral angle restraints: 5389 sinusoidal: 2542 harmonic: 2847 Sorted by residual: dihedral pdb=" O1A AGS A1201 " pdb=" O3A AGS A1201 " pdb=" PA AGS A1201 " pdb=" PB AGS A1201 " ideal model delta sinusoidal sigma weight residual -67.73 46.23 -113.96 1 3.00e+01 1.11e-03 1.50e+01 dihedral pdb=" CA GLN A 887 " pdb=" C GLN A 887 " pdb=" N PRO A 888 " pdb=" CA PRO A 888 " ideal model delta harmonic sigma weight residual 180.00 -163.70 -16.30 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CB ARG B 78 " pdb=" CG ARG B 78 " pdb=" CD ARG B 78 " pdb=" NE ARG B 78 " ideal model delta sinusoidal sigma weight residual -60.00 -118.84 58.84 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 5386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 744 0.026 - 0.053: 441 0.053 - 0.079: 143 0.079 - 0.105: 62 0.105 - 0.132: 30 Chirality restraints: 1420 Sorted by residual: chirality pdb=" CA ILE B 110 " pdb=" N ILE B 110 " pdb=" C ILE B 110 " pdb=" CB ILE B 110 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA PRO B 888 " pdb=" N PRO B 888 " pdb=" C PRO B 888 " pdb=" CB PRO B 888 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" PA AGS A1201 " pdb=" O2A AGS A1201 " pdb=" O3A AGS A1201 " pdb=" O5' AGS A1201 " both_signs ideal model delta sigma weight residual True 3.18 3.05 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 1417 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 887 " 0.031 5.00e-02 4.00e+02 4.65e-02 3.46e+00 pdb=" N PRO B 888 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 888 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 888 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 179 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO B 180 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 180 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 180 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 35 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.82e+00 pdb=" N PRO B 36 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 36 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 36 " 0.019 5.00e-02 4.00e+02 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 40 2.48 - 3.08: 5934 3.08 - 3.69: 12257 3.69 - 4.29: 17255 4.29 - 4.90: 28511 Nonbonded interactions: 63997 Sorted by model distance: nonbonded pdb=" OG1 THR B 50 " pdb="MG MG B1202 " model vdw 1.869 2.170 nonbonded pdb=" O2B AGS A1201 " pdb="MG MG A1202 " model vdw 1.929 2.170 nonbonded pdb=" OG1 THR A 50 " pdb="MG MG A1202 " model vdw 1.982 2.170 nonbonded pdb=" O2B AGS A1201 " pdb=" O2G AGS A1201 " model vdw 2.158 2.440 nonbonded pdb=" OG SER C 429 " pdb=" OE1 GLU C 432 " model vdw 2.159 2.440 ... (remaining 63992 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 10 through 242 or resid 857 through 1083 or resid 1201 thr \ ough 1202)) selection = (chain 'B' and (resid 10 through 917 or resid 929 through 1083 or resid 1201 thr \ ough 1202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 5.950 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 28.320 Find NCS groups from input model: 0.460 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.006 0.031 9177 Z= 0.378 Angle : 0.579 6.299 12645 Z= 0.320 Chirality : 0.040 0.132 1420 Planarity : 0.004 0.046 1447 Dihedral : 16.396 113.958 3555 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.85 % Allowed : 6.33 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.28), residues: 985 helix: 1.71 (0.27), residues: 394 sheet: -0.59 (0.36), residues: 204 loop : -1.73 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 128 HIS 0.005 0.001 HIS B1045 PHE 0.013 0.001 PHE B 187 TYR 0.012 0.001 TYR B 862 ARG 0.003 0.000 ARG B1059 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: A 901 HIS cc_start: 0.8663 (p-80) cc_final: 0.8447 (p-80) REVERT: C 409 ASP cc_start: 0.8641 (t0) cc_final: 0.8061 (t0) REVERT: C 476 GLN cc_start: 0.8916 (mm-40) cc_final: 0.8688 (mm110) REVERT: C 495 ILE cc_start: 0.9033 (tp) cc_final: 0.8742 (pt) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 0.2511 time to fit residues: 17.4345 Evaluate side-chains 36 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 1018 ILE Chi-restraints excluded: chain B residue 1019 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 93 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9177 Z= 0.203 Angle : 0.534 5.982 12645 Z= 0.292 Chirality : 0.038 0.138 1420 Planarity : 0.004 0.040 1447 Dihedral : 18.895 107.722 1751 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.22 % Allowed : 8.52 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.27), residues: 985 helix: 1.67 (0.27), residues: 396 sheet: -0.33 (0.37), residues: 201 loop : -1.81 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 128 HIS 0.003 0.001 HIS B1045 PHE 0.009 0.001 PHE A 221 TYR 0.011 0.001 TYR A 862 ARG 0.006 0.000 ARG A 883 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 34 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: C 409 ASP cc_start: 0.8643 (t0) cc_final: 0.8017 (t0) REVERT: C 495 ILE cc_start: 0.9006 (tp) cc_final: 0.8688 (pt) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.1935 time to fit residues: 13.0735 Evaluate side-chains 39 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 0.6980 chunk 29 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 83 optimal weight: 1.9990 chunk 92 optimal weight: 0.0970 chunk 31 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9177 Z= 0.202 Angle : 0.509 5.463 12645 Z= 0.281 Chirality : 0.037 0.134 1420 Planarity : 0.003 0.045 1447 Dihedral : 18.793 104.531 1749 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.46 % Allowed : 10.83 % Favored : 87.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.27), residues: 985 helix: 1.74 (0.27), residues: 396 sheet: -0.28 (0.36), residues: 201 loop : -1.81 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 128 HIS 0.011 0.001 HIS A 901 PHE 0.009 0.001 PHE A 221 TYR 0.011 0.001 TYR B 862 ARG 0.003 0.000 ARG A 883 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 0.858 Fit side-chains revert: symmetry clash REVERT: C 409 ASP cc_start: 0.8601 (t0) cc_final: 0.7932 (t0) outliers start: 12 outliers final: 7 residues processed: 43 average time/residue: 0.1806 time to fit residues: 12.0136 Evaluate side-chains 39 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 32 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 49 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 9177 Z= 0.430 Angle : 0.646 6.837 12645 Z= 0.346 Chirality : 0.041 0.155 1420 Planarity : 0.004 0.042 1447 Dihedral : 18.969 105.113 1749 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 1.70 % Allowed : 12.17 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.27), residues: 985 helix: 1.38 (0.27), residues: 394 sheet: -0.54 (0.36), residues: 203 loop : -2.04 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 128 HIS 0.007 0.001 HIS B1045 PHE 0.015 0.002 PHE B 187 TYR 0.014 0.002 TYR A 891 ARG 0.002 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 32 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: C 409 ASP cc_start: 0.8504 (t0) cc_final: 0.7868 (t0) outliers start: 14 outliers final: 11 residues processed: 45 average time/residue: 0.1911 time to fit residues: 13.3787 Evaluate side-chains 43 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 31 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 973 ASN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 84 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 0.0980 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9177 Z= 0.154 Angle : 0.500 6.523 12645 Z= 0.277 Chirality : 0.036 0.135 1420 Planarity : 0.003 0.040 1447 Dihedral : 18.818 97.758 1749 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.87 % Favored : 95.03 % Rotamer: Outliers : 1.34 % Allowed : 13.26 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.27), residues: 985 helix: 1.64 (0.27), residues: 397 sheet: -0.50 (0.35), residues: 204 loop : -1.80 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 128 HIS 0.002 0.000 HIS B1029 PHE 0.009 0.001 PHE A 221 TYR 0.011 0.001 TYR A 862 ARG 0.003 0.000 ARG C 410 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 35 time to evaluate : 0.986 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: B 974 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9133 (tt) REVERT: C 409 ASP cc_start: 0.8448 (t0) cc_final: 0.7775 (t0) outliers start: 11 outliers final: 7 residues processed: 45 average time/residue: 0.1785 time to fit residues: 12.5555 Evaluate side-chains 40 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 31 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 880 THR Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 0.4980 chunk 89 optimal weight: 0.7980 chunk 19 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 99 optimal weight: 7.9990 chunk 82 optimal weight: 0.1980 chunk 46 optimal weight: 0.0570 chunk 8 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9177 Z= 0.133 Angle : 0.485 10.585 12645 Z= 0.267 Chirality : 0.036 0.137 1420 Planarity : 0.003 0.044 1447 Dihedral : 18.869 97.160 1749 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.46 % Allowed : 13.50 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.27), residues: 985 helix: 1.83 (0.27), residues: 396 sheet: -0.34 (0.36), residues: 204 loop : -1.68 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.000 TRP B 128 HIS 0.003 0.000 HIS A 901 PHE 0.007 0.001 PHE A 221 TYR 0.011 0.001 TYR B 862 ARG 0.004 0.000 ARG B 969 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 35 time to evaluate : 0.882 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.7841 (mp0) REVERT: B 974 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9152 (tt) REVERT: C 409 ASP cc_start: 0.8492 (t0) cc_final: 0.7840 (t0) REVERT: C 481 ASN cc_start: 0.8173 (t0) cc_final: 0.7754 (t0) outliers start: 12 outliers final: 8 residues processed: 46 average time/residue: 0.2088 time to fit residues: 15.2772 Evaluate side-chains 43 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9177 Z= 0.234 Angle : 0.528 9.286 12645 Z= 0.286 Chirality : 0.037 0.135 1420 Planarity : 0.003 0.045 1447 Dihedral : 18.938 99.134 1748 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.34 % Allowed : 14.11 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.28), residues: 985 helix: 1.85 (0.27), residues: 396 sheet: -0.33 (0.36), residues: 204 loop : -1.73 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.003 0.001 HIS B1045 PHE 0.008 0.001 PHE B 187 TYR 0.010 0.001 TYR B 862 ARG 0.002 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.884 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7809 (mp0) REVERT: B 974 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9127 (tt) REVERT: C 409 ASP cc_start: 0.8457 (t0) cc_final: 0.7778 (t0) outliers start: 11 outliers final: 9 residues processed: 42 average time/residue: 0.1817 time to fit residues: 12.0014 Evaluate side-chains 43 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 32 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 8.9990 chunk 59 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 95 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9177 Z= 0.144 Angle : 0.482 8.180 12645 Z= 0.265 Chirality : 0.036 0.137 1420 Planarity : 0.003 0.044 1447 Dihedral : 18.844 96.126 1748 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.22 % Allowed : 14.48 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.28), residues: 985 helix: 1.89 (0.27), residues: 397 sheet: -0.22 (0.36), residues: 204 loop : -1.66 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 128 HIS 0.002 0.000 HIS B1029 PHE 0.006 0.001 PHE A 221 TYR 0.010 0.001 TYR B 862 ARG 0.002 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 153 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7622 (tt) REVERT: B 223 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7831 (mp0) REVERT: B 974 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9180 (tt) REVERT: C 409 ASP cc_start: 0.8476 (t0) cc_final: 0.7817 (t0) REVERT: C 481 ASN cc_start: 0.8179 (t0) cc_final: 0.7753 (t0) outliers start: 10 outliers final: 7 residues processed: 43 average time/residue: 0.1957 time to fit residues: 13.2491 Evaluate side-chains 43 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 33 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 0.7980 chunk 92 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.2980 chunk 28 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9177 Z= 0.184 Angle : 0.504 11.696 12645 Z= 0.273 Chirality : 0.036 0.134 1420 Planarity : 0.003 0.047 1447 Dihedral : 18.843 96.655 1748 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.46 % Allowed : 14.23 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 985 helix: 1.90 (0.27), residues: 398 sheet: -0.21 (0.36), residues: 204 loop : -1.67 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 128 HIS 0.002 0.000 HIS B1045 PHE 0.007 0.001 PHE A 221 TYR 0.010 0.001 TYR B 862 ARG 0.002 0.000 ARG C 410 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 32 time to evaluate : 0.937 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.7832 (mp0) REVERT: B 974 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9150 (tt) REVERT: C 409 ASP cc_start: 0.8437 (t0) cc_final: 0.7752 (t0) REVERT: C 481 ASN cc_start: 0.8194 (t0) cc_final: 0.7775 (t0) outliers start: 12 outliers final: 8 residues processed: 44 average time/residue: 0.1905 time to fit residues: 13.2896 Evaluate side-chains 42 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 32 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.3980 chunk 46 optimal weight: 0.3980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9177 Z= 0.162 Angle : 0.497 11.188 12645 Z= 0.269 Chirality : 0.036 0.135 1420 Planarity : 0.003 0.045 1447 Dihedral : 18.809 96.432 1748 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.34 % Allowed : 14.48 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.28), residues: 985 helix: 1.93 (0.27), residues: 397 sheet: -0.18 (0.36), residues: 204 loop : -1.66 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 128 HIS 0.002 0.000 HIS B1045 PHE 0.007 0.001 PHE A 221 TYR 0.010 0.001 TYR B 862 ARG 0.002 0.000 ARG C 410 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7855 (mp0) REVERT: B 974 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9187 (tt) REVERT: C 409 ASP cc_start: 0.8430 (t0) cc_final: 0.7745 (t0) REVERT: C 481 ASN cc_start: 0.8172 (t0) cc_final: 0.7763 (t0) outliers start: 11 outliers final: 9 residues processed: 43 average time/residue: 0.1835 time to fit residues: 12.2672 Evaluate side-chains 44 residues out of total 822 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 33 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain A residue 113 THR Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 223 GLU Chi-restraints excluded: chain B residue 227 ASP Chi-restraints excluded: chain B residue 974 LEU Chi-restraints excluded: chain B residue 1019 VAL Chi-restraints excluded: chain B residue 1047 VAL Chi-restraints excluded: chain B residue 1078 VAL Chi-restraints excluded: chain C residue 474 ASP Chi-restraints excluded: chain C residue 492 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 84 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 71 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.065116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.045106 restraints weight = 30862.199| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.37 r_work: 0.2649 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9177 Z= 0.181 Angle : 0.504 11.143 12645 Z= 0.272 Chirality : 0.036 0.135 1420 Planarity : 0.003 0.046 1447 Dihedral : 18.791 96.460 1748 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.46 % Allowed : 14.11 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.28), residues: 985 helix: 1.90 (0.27), residues: 399 sheet: -0.20 (0.36), residues: 204 loop : -1.68 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 128 HIS 0.002 0.000 HIS B1045 PHE 0.006 0.001 PHE A 221 TYR 0.010 0.001 TYR B 862 ARG 0.002 0.000 ARG C 410 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1690.50 seconds wall clock time: 31 minutes 27.50 seconds (1887.50 seconds total)