Starting phenix.real_space_refine on Tue Jul 29 22:49:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6se0_10151/07_2025/6se0_10151.cif Found real_map, /net/cci-nas-00/data/ceres_data/6se0_10151/07_2025/6se0_10151.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6se0_10151/07_2025/6se0_10151.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6se0_10151/07_2025/6se0_10151.map" model { file = "/net/cci-nas-00/data/ceres_data/6se0_10151/07_2025/6se0_10151.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6se0_10151/07_2025/6se0_10151.cif" } resolution = 3.8 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= 0.003 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: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6657 2.51 5 N 2256 2.21 5 O 2791 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12002 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 845 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 8.39, per 1000 atoms: 0.70 Number of scatterers: 12002 At special positions: 0 Unit cell: (75.26, 119.78, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2791 8.00 N 2256 7.00 C 6657 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 992.1 milliseconds 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1414 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 9 sheets defined 70.8% alpha, 2.6% beta 145 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 6.12 Creating SS restraints... Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.806A pdb=" N GLU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.824A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LYS A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.509A pdb=" N ALA A 116 " --> pdb=" O LEU A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 134 through 139 removed outlier: 3.783A pdb=" N LEU A 139 " --> pdb=" O LEU A 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.593A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.202A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.583A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.616A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 3.700A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 removed outlier: 3.664A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.547A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.520A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 3.522A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.838A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 116 removed outlier: 3.602A pdb=" N LEU E 91 " --> pdb=" O GLN E 87 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.804A pdb=" N GLY E 134 " --> pdb=" O ARG E 130 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.542A pdb=" N GLY F 28 " --> pdb=" O ASN F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.289A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 removed outlier: 3.509A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.799A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.550A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.582A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (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 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.577A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 122 removed outlier: 3.591A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.240A pdb=" N ASN A 85 " --> 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 120 through 121 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.870A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.015A pdb=" N ASN E 85 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.527A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 377 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 368 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 4.68 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2004 1.33 - 1.45: 4338 1.45 - 1.57: 5874 1.57 - 1.68: 576 1.68 - 1.80: 18 Bond restraints: 12810 Sorted by residual: bond pdb=" C3' DA J 6 " pdb=" O3' DA J 6 " ideal model delta sigma weight residual 1.422 1.358 0.064 3.00e-02 1.11e+03 4.55e+00 bond pdb=" SD MET G 51 " pdb=" CE MET G 51 " ideal model delta sigma weight residual 1.791 1.738 0.053 2.50e-02 1.60e+03 4.46e+00 bond pdb=" CG1 ILE A 132 " pdb=" CD1 ILE A 132 " ideal model delta sigma weight residual 1.513 1.441 0.072 3.90e-02 6.57e+02 3.41e+00 bond pdb=" CB ILE A 51 " pdb=" CG2 ILE A 51 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.23e+00 bond pdb=" CB TRP E 86 " pdb=" CG TRP E 86 " ideal model delta sigma weight residual 1.498 1.444 0.054 3.10e-02 1.04e+03 3.07e+00 ... (remaining 12805 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.52: 18371 3.52 - 7.04: 145 7.04 - 10.57: 17 10.57 - 14.09: 1 14.09 - 17.61: 1 Bond angle restraints: 18535 Sorted by residual: angle pdb=" CA LEU F 90 " pdb=" CB LEU F 90 " pdb=" CG LEU F 90 " ideal model delta sigma weight residual 116.30 98.69 17.61 3.50e+00 8.16e-02 2.53e+01 angle pdb=" CB MET G 51 " pdb=" CG MET G 51 " pdb=" SD MET G 51 " ideal model delta sigma weight residual 112.70 126.00 -13.30 3.00e+00 1.11e-01 1.97e+01 angle pdb=" C ILE G 87 " pdb=" N ARG G 88 " pdb=" CA ARG G 88 " ideal model delta sigma weight residual 121.94 114.53 7.41 2.00e+00 2.50e-01 1.37e+01 angle pdb=" CA VAL C 107 " pdb=" CB VAL C 107 " pdb=" CG1 VAL C 107 " ideal model delta sigma weight residual 110.40 116.30 -5.90 1.70e+00 3.46e-01 1.21e+01 angle pdb=" CA ARG E 43 " pdb=" CB ARG E 43 " pdb=" CG ARG E 43 " ideal model delta sigma weight residual 114.10 120.97 -6.87 2.00e+00 2.50e-01 1.18e+01 ... (remaining 18530 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.26: 5109 29.26 - 58.52: 1726 58.52 - 87.78: 87 87.78 - 117.04: 3 117.04 - 146.30: 1 Dihedral angle restraints: 6926 sinusoidal: 4729 harmonic: 2197 Sorted by residual: dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual 180.00 -160.46 -19.54 0 5.00e+00 4.00e-02 1.53e+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 73.70 146.30 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" CA GLN G 112 " pdb=" C GLN G 112 " pdb=" N ALA G 113 " pdb=" CA ALA G 113 " ideal model delta harmonic sigma weight residual -180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 6923 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1514 0.058 - 0.116: 486 0.116 - 0.175: 86 0.175 - 0.233: 9 0.233 - 0.291: 4 Chirality restraints: 2099 Sorted by residual: chirality pdb=" CG LEU G 108 " pdb=" CB LEU G 108 " pdb=" CD1 LEU G 108 " pdb=" CD2 LEU G 108 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" P DG J 50 " pdb=" OP1 DG J 50 " pdb=" OP2 DG J 50 " pdb=" O5' DG J 50 " both_signs ideal model delta sigma weight residual True 2.35 -2.60 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.62e+00 ... (remaining 2096 not shown) Planarity restraints: 1338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.063 5.00e-02 4.00e+02 9.47e-02 1.44e+01 pdb=" N PRO G 80 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO C 80 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 119 " 0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C VAL A 119 " -0.057 2.00e-02 2.50e+03 pdb=" O VAL A 119 " 0.020 2.00e-02 2.50e+03 pdb=" N THR A 120 " 0.019 2.00e-02 2.50e+03 ... (remaining 1335 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2322 2.78 - 3.31: 10081 3.31 - 3.84: 23976 3.84 - 4.37: 26839 4.37 - 4.90: 37586 Nonbonded interactions: 100804 Sorted by model distance: nonbonded pdb=" OG SER G 18 " pdb=" O LEU G 23 " model vdw 2.248 3.040 nonbonded pdb=" O2 DC I -56 " pdb=" N2 DG J 56 " model vdw 2.286 2.496 nonbonded pdb=" O2 DC I -62 " pdb=" N2 DG J 62 " model vdw 2.299 2.496 nonbonded pdb=" OH TYR H 40 " pdb=" OP1 DG I 48 " model vdw 2.319 3.040 nonbonded pdb=" OG1 THR E 113 " pdb=" O THR E 120 " model vdw 2.343 3.040 ... (remaining 100799 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 116) selection = (chain 'G' and resid 10 through 116) } ncs_group { reference = (chain 'D' and resid 31 through 124) selection = chain 'H' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 35.530 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.009 0.074 12810 Z= 0.378 Angle : 1.012 17.610 18535 Z= 0.574 Chirality : 0.057 0.291 2099 Planarity : 0.008 0.095 1338 Dihedral : 28.079 146.298 5512 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.23), residues: 749 helix: -1.67 (0.17), residues: 511 sheet: None (None), residues: 0 loop : -1.94 (0.31), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 86 HIS 0.015 0.003 HIS F 75 PHE 0.025 0.004 PHE A 78 TYR 0.035 0.004 TYR A 110 ARG 0.011 0.001 ARG A 44 Details of bonding type rmsd hydrogen bonds : bond 0.12059 ( 745) hydrogen bonds : angle 4.17951 ( 1847) covalent geometry : bond 0.00850 (12810) covalent geometry : angle 1.01243 (18535) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 0.953 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9426 (tp30) cc_final: 0.9176 (tp30) REVERT: A 85 ASN cc_start: 0.8494 (m-40) cc_final: 0.8198 (m-40) REVERT: B 45 ARG cc_start: 0.7613 (mtm180) cc_final: 0.6389 (ttm110) REVERT: B 79 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7575 (mtmm) REVERT: C 56 GLU cc_start: 0.6795 (tt0) cc_final: 0.6576 (tt0) REVERT: C 57 TYR cc_start: 0.9003 (t80) cc_final: 0.8528 (t80) REVERT: C 61 GLU cc_start: 0.8731 (tp30) cc_final: 0.8261 (tp30) REVERT: C 92 GLU cc_start: 0.8295 (tt0) cc_final: 0.7903 (tt0) REVERT: C 95 LYS cc_start: 0.8448 (ttmt) cc_final: 0.7929 (tppt) REVERT: D 113 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7848 (mt-10) REVERT: D 116 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8555 (ttmm) REVERT: E 49 LYS cc_start: 0.8950 (ptmt) cc_final: 0.8452 (ptmt) REVERT: E 64 LYS cc_start: 0.7947 (mtpt) cc_final: 0.7371 (tptt) REVERT: E 73 GLU cc_start: 0.9093 (tp30) cc_final: 0.8453 (tp30) REVERT: G 71 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.7999 (mtm180) REVERT: G 92 GLU cc_start: 0.8177 (tt0) cc_final: 0.7792 (tt0) REVERT: H 93 GLU cc_start: 0.8349 (mm-30) cc_final: 0.8066 (mm-30) REVERT: H 95 GLN cc_start: 0.8108 (tt0) cc_final: 0.7145 (tm-30) REVERT: H 105 GLU cc_start: 0.8171 (tp30) cc_final: 0.7551 (tp30) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.3666 time to fit residues: 122.0888 Evaluate side-chains 185 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 42 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 8.9990 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 95 GLN A 104 HIS B 64 ASN D 95 GLN G 31 HIS G 73 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.130005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.093481 restraints weight = 32494.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.097049 restraints weight = 16201.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.099436 restraints weight = 10327.159| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12810 Z= 0.164 Angle : 0.625 8.816 18535 Z= 0.363 Chirality : 0.034 0.153 2099 Planarity : 0.005 0.071 1338 Dihedral : 30.080 147.477 4015 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 4.15 % Allowed : 20.10 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.27), residues: 749 helix: 0.34 (0.20), residues: 542 sheet: None (None), residues: 0 loop : -1.53 (0.35), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP E 47 HIS 0.005 0.001 HIS E 115 PHE 0.009 0.001 PHE G 25 TYR 0.017 0.002 TYR H 83 ARG 0.006 0.001 ARG E 131 Details of bonding type rmsd hydrogen bonds : bond 0.04631 ( 745) hydrogen bonds : angle 3.02731 ( 1847) covalent geometry : bond 0.00348 (12810) covalent geometry : angle 0.62526 (18535) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.9360 (tp30) cc_final: 0.9133 (tp30) REVERT: B 44 LYS cc_start: 0.8525 (tttt) cc_final: 0.7997 (mmmm) REVERT: B 45 ARG cc_start: 0.7325 (mtm180) cc_final: 0.6338 (mtt90) REVERT: B 84 MET cc_start: 0.8015 (OUTLIER) cc_final: 0.7466 (mtm) REVERT: C 56 GLU cc_start: 0.6628 (tt0) cc_final: 0.6339 (tt0) REVERT: C 57 TYR cc_start: 0.8929 (t80) cc_final: 0.8387 (t80) REVERT: D 76 GLU cc_start: 0.8348 (tp30) cc_final: 0.8103 (tp30) REVERT: D 106 LEU cc_start: 0.9561 (tp) cc_final: 0.9257 (tp) REVERT: D 113 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7706 (mt-10) REVERT: E 49 LYS cc_start: 0.9017 (ptmt) cc_final: 0.8395 (ptmt) REVERT: E 73 GLU cc_start: 0.8996 (tp30) cc_final: 0.8296 (tm-30) REVERT: G 71 ARG cc_start: 0.8715 (mmm-85) cc_final: 0.8302 (ttm110) REVERT: G 92 GLU cc_start: 0.8097 (tt0) cc_final: 0.7812 (tt0) REVERT: H 93 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7949 (mm-30) REVERT: H 95 GLN cc_start: 0.8014 (tt0) cc_final: 0.7019 (tm-30) REVERT: H 105 GLU cc_start: 0.7911 (tp30) cc_final: 0.7525 (tp30) outliers start: 26 outliers final: 11 residues processed: 221 average time/residue: 0.2674 time to fit residues: 80.9049 Evaluate side-chains 186 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 10 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 0.1980 chunk 93 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 87 optimal weight: 20.0000 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.125562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.089301 restraints weight = 34382.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.092541 restraints weight = 17594.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.094667 restraints weight = 11466.491| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12810 Z= 0.230 Angle : 0.675 12.019 18535 Z= 0.386 Chirality : 0.036 0.150 2099 Planarity : 0.005 0.056 1338 Dihedral : 30.153 147.390 4015 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 6.06 % Allowed : 22.65 % Favored : 71.29 % 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: 0.33 (0.29), residues: 749 helix: 0.85 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -1.40 (0.36), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP E 47 HIS 0.007 0.001 HIS F 75 PHE 0.013 0.002 PHE B 100 TYR 0.017 0.003 TYR F 88 ARG 0.003 0.001 ARG B 35 Details of bonding type rmsd hydrogen bonds : bond 0.05104 ( 745) hydrogen bonds : angle 3.23547 ( 1847) covalent geometry : bond 0.00503 (12810) covalent geometry : angle 0.67531 (18535) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 181 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8117 (ttpp) REVERT: A 110 TYR cc_start: 0.7492 (t80) cc_final: 0.7158 (t80) REVERT: B 45 ARG cc_start: 0.7487 (mtm180) cc_final: 0.6951 (mtt90) REVERT: B 51 TYR cc_start: 0.8138 (m-80) cc_final: 0.7653 (m-80) REVERT: B 84 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7324 (mtm) REVERT: C 56 GLU cc_start: 0.6676 (tt0) cc_final: 0.6403 (tt0) REVERT: C 57 TYR cc_start: 0.8968 (t80) cc_final: 0.8270 (t80) REVERT: C 61 GLU cc_start: 0.8623 (tp30) cc_final: 0.8227 (tm-30) REVERT: D 76 GLU cc_start: 0.8169 (tp30) cc_final: 0.7899 (tp30) REVERT: D 79 ARG cc_start: 0.8052 (ptp90) cc_final: 0.6798 (ptp90) REVERT: D 113 GLU cc_start: 0.7914 (mt-10) cc_final: 0.7701 (mt-10) REVERT: D 120 LYS cc_start: 0.8690 (ttmm) cc_final: 0.8127 (tttm) REVERT: E 49 LYS cc_start: 0.9017 (ptmt) cc_final: 0.8462 (ptmt) REVERT: E 73 GLU cc_start: 0.9101 (tp30) cc_final: 0.8390 (tm-30) REVERT: E 110 TYR cc_start: 0.6980 (t80) cc_final: 0.6770 (t80) REVERT: F 53 GLU cc_start: 0.8206 (tt0) cc_final: 0.7826 (tt0) REVERT: G 71 ARG cc_start: 0.8711 (mmm-85) cc_final: 0.7937 (ptp-110) REVERT: G 92 GLU cc_start: 0.8159 (tt0) cc_final: 0.7944 (tt0) REVERT: H 93 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7832 (mm-30) REVERT: H 95 GLN cc_start: 0.8123 (tt0) cc_final: 0.7248 (tm-30) outliers start: 38 outliers final: 23 residues processed: 196 average time/residue: 0.3356 time to fit residues: 91.6817 Evaluate side-chains 192 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 120 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.124038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.086594 restraints weight = 34577.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.089559 restraints weight = 18316.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.091561 restraints weight = 12187.081| |-----------------------------------------------------------------------------| r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.070 12810 Z= 0.409 Angle : 0.858 17.660 18535 Z= 0.479 Chirality : 0.045 0.167 2099 Planarity : 0.006 0.056 1338 Dihedral : 30.843 148.631 4015 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 9.09 % Allowed : 22.33 % Favored : 68.58 % 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: -0.55 (0.28), residues: 749 helix: 0.27 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -1.84 (0.34), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 47 HIS 0.008 0.002 HIS E 115 PHE 0.028 0.003 PHE A 84 TYR 0.048 0.004 TYR H 83 ARG 0.005 0.001 ARG H 72 Details of bonding type rmsd hydrogen bonds : bond 0.07131 ( 745) hydrogen bonds : angle 4.31824 ( 1847) covalent geometry : bond 0.00898 (12810) covalent geometry : angle 0.85760 (18535) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 169 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8044 (ttpp) REVERT: B 45 ARG cc_start: 0.7713 (mtm180) cc_final: 0.6690 (tpp80) REVERT: B 51 TYR cc_start: 0.8202 (m-80) cc_final: 0.7853 (m-80) REVERT: C 42 ARG cc_start: 0.7957 (mtp85) cc_final: 0.7722 (mtm-85) REVERT: C 57 TYR cc_start: 0.8988 (t80) cc_final: 0.8771 (t80) REVERT: C 64 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7773 (mm-30) REVERT: C 87 ILE cc_start: 0.9441 (tp) cc_final: 0.9179 (tp) REVERT: D 59 MET cc_start: 0.8128 (tpp) cc_final: 0.7774 (tpp) REVERT: D 106 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9401 (mt) REVERT: E 49 LYS cc_start: 0.9106 (ptmt) cc_final: 0.8668 (ptmt) REVERT: E 73 GLU cc_start: 0.9166 (tp30) cc_final: 0.8409 (tm-30) REVERT: E 110 TYR cc_start: 0.7596 (t80) cc_final: 0.7207 (t80) REVERT: F 31 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7701 (pttt) REVERT: F 53 GLU cc_start: 0.8191 (tt0) cc_final: 0.7737 (tt0) REVERT: F 88 TYR cc_start: 0.8620 (m-10) cc_final: 0.8368 (m-80) REVERT: G 71 ARG cc_start: 0.8792 (mmm-85) cc_final: 0.8249 (ttm110) REVERT: G 92 GLU cc_start: 0.8326 (tt0) cc_final: 0.7980 (tt0) REVERT: H 93 GLU cc_start: 0.8578 (mm-30) cc_final: 0.7943 (mm-30) REVERT: H 108 LYS cc_start: 0.8871 (mmmt) cc_final: 0.8523 (mmtt) outliers start: 57 outliers final: 40 residues processed: 196 average time/residue: 0.3833 time to fit residues: 102.9999 Evaluate side-chains 202 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 159 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 78 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 33 ARG Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 111 VAL Chi-restraints excluded: chain H residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 95 optimal weight: 5.9990 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 78 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.130111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.092928 restraints weight = 33543.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.096304 restraints weight = 17284.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.098563 restraints weight = 11179.389| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12810 Z= 0.173 Angle : 0.644 11.907 18535 Z= 0.369 Chirality : 0.035 0.152 2099 Planarity : 0.004 0.054 1338 Dihedral : 30.506 146.624 4015 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.99 % Allowed : 30.94 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.29), residues: 749 helix: 0.92 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.66 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE H 65 TYR 0.026 0.002 TYR H 83 ARG 0.006 0.000 ARG D 86 Details of bonding type rmsd hydrogen bonds : bond 0.04733 ( 745) hydrogen bonds : angle 3.15455 ( 1847) covalent geometry : bond 0.00374 (12810) covalent geometry : angle 0.64383 (18535) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 TYR cc_start: 0.7434 (t80) cc_final: 0.6516 (t80) REVERT: B 24 ASP cc_start: 0.7898 (t0) cc_final: 0.7509 (p0) REVERT: B 44 LYS cc_start: 0.8511 (tttt) cc_final: 0.8108 (pttt) REVERT: B 45 ARG cc_start: 0.7527 (mtm180) cc_final: 0.6997 (mtt90) REVERT: B 51 TYR cc_start: 0.8024 (m-80) cc_final: 0.7574 (m-80) REVERT: B 53 GLU cc_start: 0.8191 (tp30) cc_final: 0.7962 (tp30) REVERT: B 84 MET cc_start: 0.7695 (mmp) cc_final: 0.7139 (mtm) REVERT: B 98 TYR cc_start: 0.8279 (m-10) cc_final: 0.8058 (m-80) REVERT: C 61 GLU cc_start: 0.8685 (tp30) cc_final: 0.8123 (tm-30) REVERT: C 64 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7816 (mm-30) REVERT: D 59 MET cc_start: 0.7968 (tpp) cc_final: 0.7538 (tpp) REVERT: D 86 ARG cc_start: 0.8019 (mmp80) cc_final: 0.7707 (mmp80) REVERT: E 49 LYS cc_start: 0.9041 (ptmt) cc_final: 0.8554 (ptmt) REVERT: E 61 LEU cc_start: 0.9112 (OUTLIER) cc_final: 0.8698 (pp) REVERT: E 73 GLU cc_start: 0.9128 (tp30) cc_final: 0.8396 (tm-30) REVERT: E 110 TYR cc_start: 0.7004 (t80) cc_final: 0.6710 (t80) REVERT: F 50 ILE cc_start: 0.8726 (tp) cc_final: 0.8153 (mm) REVERT: F 53 GLU cc_start: 0.8088 (tt0) cc_final: 0.7666 (tt0) REVERT: G 71 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.7925 (ptp-110) REVERT: H 93 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7766 (mm-30) REVERT: H 95 GLN cc_start: 0.8173 (tt0) cc_final: 0.7284 (tm-30) outliers start: 25 outliers final: 18 residues processed: 197 average time/residue: 0.2505 time to fit residues: 68.8441 Evaluate side-chains 185 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 64 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 5.9990 chunk 53 optimal weight: 5.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 HIS G 68 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.125091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.091769 restraints weight = 32161.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.095029 restraints weight = 16308.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.097199 restraints weight = 10426.594| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12810 Z= 0.157 Angle : 0.615 9.017 18535 Z= 0.352 Chirality : 0.034 0.158 2099 Planarity : 0.004 0.053 1338 Dihedral : 30.217 145.121 4015 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.99 % Allowed : 30.78 % Favored : 65.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.30), residues: 749 helix: 1.32 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -1.55 (0.35), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.010 0.001 PHE H 65 TYR 0.037 0.002 TYR C 57 ARG 0.003 0.000 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.04475 ( 745) hydrogen bonds : angle 2.96249 ( 1847) covalent geometry : bond 0.00337 (12810) covalent geometry : angle 0.61495 (18535) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 TYR cc_start: 0.7336 (t80) cc_final: 0.6743 (t80) REVERT: B 24 ASP cc_start: 0.7613 (t0) cc_final: 0.7345 (p0) REVERT: B 29 ILE cc_start: 0.7886 (mm) cc_final: 0.7487 (mp) REVERT: B 44 LYS cc_start: 0.8538 (tttt) cc_final: 0.8092 (pttt) REVERT: B 45 ARG cc_start: 0.7264 (mtm180) cc_final: 0.6422 (mtt90) REVERT: B 84 MET cc_start: 0.7656 (mmp) cc_final: 0.7100 (mtm) REVERT: B 98 TYR cc_start: 0.8212 (m-10) cc_final: 0.7986 (m-80) REVERT: C 61 GLU cc_start: 0.8542 (tp30) cc_final: 0.8052 (tm-30) REVERT: C 64 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7831 (mm-30) REVERT: D 59 MET cc_start: 0.7871 (tpp) cc_final: 0.7417 (tpp) REVERT: D 86 ARG cc_start: 0.8243 (mmp80) cc_final: 0.7937 (mmp80) REVERT: E 49 LYS cc_start: 0.9002 (ptmt) cc_final: 0.8495 (ptmt) REVERT: E 61 LEU cc_start: 0.8839 (pt) cc_final: 0.8377 (pp) REVERT: E 73 GLU cc_start: 0.9086 (tp30) cc_final: 0.8290 (tm-30) REVERT: E 110 TYR cc_start: 0.6866 (t80) cc_final: 0.6591 (t80) REVERT: E 127 GLN cc_start: 0.8334 (tt0) cc_final: 0.7796 (tp40) REVERT: F 31 LYS cc_start: 0.7813 (OUTLIER) cc_final: 0.7530 (tttt) REVERT: F 53 GLU cc_start: 0.8022 (tt0) cc_final: 0.7730 (tt0) REVERT: F 93 GLN cc_start: 0.8530 (OUTLIER) cc_final: 0.8092 (tt0) REVERT: G 71 ARG cc_start: 0.8753 (mmm-85) cc_final: 0.8278 (ttm110) REVERT: H 93 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7803 (mm-30) REVERT: H 95 GLN cc_start: 0.8061 (tt0) cc_final: 0.7170 (tm-30) outliers start: 25 outliers final: 19 residues processed: 194 average time/residue: 0.2732 time to fit residues: 75.1382 Evaluate side-chains 192 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 171 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 17 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 52 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 82 HIS G 68 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.132218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.094953 restraints weight = 33984.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.098347 restraints weight = 17538.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.100632 restraints weight = 11349.418| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12810 Z= 0.178 Angle : 0.623 9.572 18535 Z= 0.357 Chirality : 0.034 0.170 2099 Planarity : 0.004 0.053 1338 Dihedral : 30.233 145.197 4015 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.83 % Allowed : 31.10 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.30), residues: 749 helix: 1.31 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.51 (0.35), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 47 HIS 0.006 0.001 HIS F 75 PHE 0.017 0.001 PHE E 67 TYR 0.031 0.003 TYR D 40 ARG 0.003 0.000 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.04613 ( 745) hydrogen bonds : angle 3.09687 ( 1847) covalent geometry : bond 0.00388 (12810) covalent geometry : angle 0.62250 (18535) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 181 time to evaluate : 1.322 Fit side-chains revert: symmetry clash REVERT: A 110 TYR cc_start: 0.7346 (t80) cc_final: 0.6550 (t80) REVERT: B 24 ASP cc_start: 0.7812 (t0) cc_final: 0.7430 (p0) REVERT: B 29 ILE cc_start: 0.7939 (mm) cc_final: 0.7591 (mp) REVERT: B 44 LYS cc_start: 0.8539 (tttt) cc_final: 0.8134 (pttt) REVERT: B 45 ARG cc_start: 0.7320 (mtm180) cc_final: 0.6327 (mtt90) REVERT: B 84 MET cc_start: 0.7719 (mmp) cc_final: 0.7071 (mtm) REVERT: B 98 TYR cc_start: 0.8215 (m-10) cc_final: 0.7999 (m-80) REVERT: C 61 GLU cc_start: 0.8515 (tp30) cc_final: 0.8030 (tm-30) REVERT: C 64 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7852 (mm-30) REVERT: D 86 ARG cc_start: 0.8309 (mmp80) cc_final: 0.7873 (mmp80) REVERT: E 49 LYS cc_start: 0.9007 (ptmt) cc_final: 0.8773 (ptmt) REVERT: E 61 LEU cc_start: 0.8898 (pt) cc_final: 0.8589 (pp) REVERT: E 73 GLU cc_start: 0.9101 (tp30) cc_final: 0.8271 (tm-30) REVERT: E 110 TYR cc_start: 0.7067 (t80) cc_final: 0.6728 (t80) REVERT: E 127 GLN cc_start: 0.8373 (tt0) cc_final: 0.7861 (tp40) REVERT: F 31 LYS cc_start: 0.7793 (OUTLIER) cc_final: 0.7454 (tttt) REVERT: F 53 GLU cc_start: 0.8053 (tt0) cc_final: 0.7781 (tt0) REVERT: G 71 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8297 (ttm110) REVERT: H 93 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7783 (mm-30) REVERT: H 95 GLN cc_start: 0.8037 (tt0) cc_final: 0.7191 (tm-30) outliers start: 24 outliers final: 19 residues processed: 192 average time/residue: 0.2531 time to fit residues: 69.1633 Evaluate side-chains 189 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 169 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 57 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 3 optimal weight: 0.0000 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 7.9990 chunk 90 optimal weight: 8.9990 chunk 24 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN G 68 ASN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.128140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.095597 restraints weight = 32111.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.098965 restraints weight = 16333.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.101223 restraints weight = 10368.798| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12810 Z= 0.152 Angle : 0.609 8.364 18535 Z= 0.347 Chirality : 0.033 0.159 2099 Planarity : 0.004 0.056 1338 Dihedral : 30.059 144.403 4015 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.71 % Allowed : 32.38 % Favored : 64.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.30), residues: 749 helix: 1.38 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -1.43 (0.36), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.042 0.002 TYR H 83 ARG 0.004 0.000 ARG E 52 Details of bonding type rmsd hydrogen bonds : bond 0.04356 ( 745) hydrogen bonds : angle 2.91695 ( 1847) covalent geometry : bond 0.00324 (12810) covalent geometry : angle 0.60896 (18535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 2.062 Fit side-chains revert: symmetry clash REVERT: A 110 TYR cc_start: 0.7131 (t80) cc_final: 0.6717 (t80) REVERT: B 29 ILE cc_start: 0.7830 (mm) cc_final: 0.7490 (mp) REVERT: B 44 LYS cc_start: 0.8619 (tttt) cc_final: 0.8210 (pttt) REVERT: B 45 ARG cc_start: 0.7008 (mtm180) cc_final: 0.6255 (mtt90) REVERT: B 81 VAL cc_start: 0.8644 (t) cc_final: 0.8402 (p) REVERT: B 84 MET cc_start: 0.7707 (mmp) cc_final: 0.7077 (mtm) REVERT: C 61 GLU cc_start: 0.8546 (tp30) cc_final: 0.7896 (tm-30) REVERT: C 64 GLU cc_start: 0.8404 (mm-30) cc_final: 0.7717 (mm-30) REVERT: C 65 LEU cc_start: 0.9381 (mp) cc_final: 0.8840 (mp) REVERT: E 49 LYS cc_start: 0.8974 (ptmt) cc_final: 0.8436 (ptmt) REVERT: E 73 GLU cc_start: 0.9070 (tp30) cc_final: 0.8209 (tm-30) REVERT: E 110 TYR cc_start: 0.6822 (t80) cc_final: 0.6526 (t80) REVERT: E 127 GLN cc_start: 0.8361 (tt0) cc_final: 0.7895 (tp40) REVERT: F 31 LYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7392 (tttt) REVERT: F 53 GLU cc_start: 0.8147 (tt0) cc_final: 0.7848 (tt0) REVERT: F 93 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7954 (tt0) REVERT: G 71 ARG cc_start: 0.8687 (mmm-85) cc_final: 0.7837 (ptp-110) REVERT: G 92 GLU cc_start: 0.8624 (mp0) cc_final: 0.7955 (mt-10) REVERT: H 93 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7882 (mm-30) REVERT: H 95 GLN cc_start: 0.8097 (tt0) cc_final: 0.7228 (tm-30) outliers start: 17 outliers final: 13 residues processed: 199 average time/residue: 0.2993 time to fit residues: 84.8263 Evaluate side-chains 189 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 1.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 111 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 54 optimal weight: 6.9990 chunk 20 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 92 optimal weight: 8.9990 chunk 81 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 overall best weight: 5.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 89 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.118736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.085479 restraints weight = 33190.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.088332 restraints weight = 17476.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.090224 restraints weight = 11517.445| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 12810 Z= 0.340 Angle : 0.785 13.996 18535 Z= 0.442 Chirality : 0.041 0.164 2099 Planarity : 0.006 0.048 1338 Dihedral : 30.674 146.876 4015 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 4.47 % Allowed : 31.58 % Favored : 63.96 % 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: 0.07 (0.29), residues: 749 helix: 0.70 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.51 (0.35), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP E 47 HIS 0.009 0.002 HIS F 75 PHE 0.024 0.003 PHE A 84 TYR 0.096 0.005 TYR H 83 ARG 0.009 0.001 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.06319 ( 745) hydrogen bonds : angle 3.94277 ( 1847) covalent geometry : bond 0.00753 (12810) covalent geometry : angle 0.78513 (18535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 44 LYS cc_start: 0.8439 (tttt) cc_final: 0.8210 (pttt) REVERT: B 45 ARG cc_start: 0.7595 (mtm180) cc_final: 0.6427 (ttm170) REVERT: B 51 TYR cc_start: 0.8143 (m-80) cc_final: 0.7775 (m-80) REVERT: C 64 GLU cc_start: 0.8514 (mm-30) cc_final: 0.7838 (mm-30) REVERT: C 90 ASP cc_start: 0.6982 (t70) cc_final: 0.5862 (t0) REVERT: D 59 MET cc_start: 0.8052 (tpp) cc_final: 0.7621 (tpp) REVERT: E 49 LYS cc_start: 0.8999 (ptmt) cc_final: 0.8515 (ptmt) REVERT: E 61 LEU cc_start: 0.9225 (pt) cc_final: 0.8881 (pp) REVERT: E 73 GLU cc_start: 0.9146 (tp30) cc_final: 0.8348 (tm-30) REVERT: F 31 LYS cc_start: 0.7788 (OUTLIER) cc_final: 0.7459 (tttm) REVERT: F 53 GLU cc_start: 0.8093 (tt0) cc_final: 0.7766 (tt0) REVERT: G 71 ARG cc_start: 0.8761 (mmm-85) cc_final: 0.7864 (mtm-85) REVERT: G 92 GLU cc_start: 0.8728 (mp0) cc_final: 0.8057 (mt-10) REVERT: H 93 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7839 (mm-30) outliers start: 28 outliers final: 22 residues processed: 170 average time/residue: 0.3101 time to fit residues: 75.3553 Evaluate side-chains 172 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 122 PHE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 89 ASN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain E residue 122 PHE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 78 SER Chi-restraints excluded: chain H residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 chunk 3 optimal weight: 0.0370 chunk 26 optimal weight: 6.9990 chunk 2 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 78 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** E 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.127953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.092602 restraints weight = 34088.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.095888 restraints weight = 17217.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.098102 restraints weight = 11047.889| |-----------------------------------------------------------------------------| r_work (final): 0.3750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12810 Z= 0.164 Angle : 0.662 10.460 18535 Z= 0.369 Chirality : 0.035 0.184 2099 Planarity : 0.004 0.051 1338 Dihedral : 30.365 145.349 4015 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.03 % Allowed : 33.97 % Favored : 63.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.30), residues: 749 helix: 1.03 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -1.41 (0.35), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.024 0.002 PHE E 67 TYR 0.062 0.003 TYR H 83 ARG 0.003 0.000 ARG B 95 Details of bonding type rmsd hydrogen bonds : bond 0.04606 ( 745) hydrogen bonds : angle 3.17191 ( 1847) covalent geometry : bond 0.00358 (12810) covalent geometry : angle 0.66233 (18535) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1498 Ramachandran restraints generated. 749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 176 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 110 TYR cc_start: 0.7235 (t80) cc_final: 0.6620 (t80) REVERT: A 128 LEU cc_start: 0.8398 (tt) cc_final: 0.8114 (tp) REVERT: B 29 ILE cc_start: 0.7703 (mm) cc_final: 0.7162 (mp) REVERT: B 44 LYS cc_start: 0.8439 (tttt) cc_final: 0.8018 (pttt) REVERT: B 84 MET cc_start: 0.7502 (mmp) cc_final: 0.6979 (mtm) REVERT: C 61 GLU cc_start: 0.8558 (tp30) cc_final: 0.7993 (tm-30) REVERT: C 64 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7846 (mm-30) REVERT: D 59 MET cc_start: 0.7860 (tpp) cc_final: 0.7375 (tpp) REVERT: E 49 LYS cc_start: 0.8879 (ptmt) cc_final: 0.8375 (ptmt) REVERT: E 61 LEU cc_start: 0.8865 (pt) cc_final: 0.8423 (pp) REVERT: E 73 GLU cc_start: 0.9080 (tp30) cc_final: 0.8273 (tm-30) REVERT: E 110 TYR cc_start: 0.7016 (t80) cc_final: 0.6643 (t80) REVERT: F 31 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7394 (tttt) REVERT: F 53 GLU cc_start: 0.8093 (tt0) cc_final: 0.7707 (tt0) REVERT: F 84 MET cc_start: 0.7138 (mmp) cc_final: 0.6643 (mmp) REVERT: F 93 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: G 61 GLU cc_start: 0.8634 (tp30) cc_final: 0.8429 (tp30) REVERT: G 71 ARG cc_start: 0.8652 (mmm-85) cc_final: 0.7701 (ptp-170) REVERT: G 92 GLU cc_start: 0.8697 (mp0) cc_final: 0.8246 (pm20) REVERT: H 93 GLU cc_start: 0.8394 (mm-30) cc_final: 0.7824 (mm-30) REVERT: H 95 GLN cc_start: 0.8187 (tt0) cc_final: 0.7336 (tm-30) outliers start: 19 outliers final: 13 residues processed: 185 average time/residue: 0.2917 time to fit residues: 76.7308 Evaluate side-chains 186 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 111 ILE Chi-restraints excluded: chain H residue 78 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 21 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.1980 chunk 73 optimal weight: 20.0000 chunk 39 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.134754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.098315 restraints weight = 33821.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.101766 restraints weight = 17258.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.104090 restraints weight = 11074.775| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.4746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12810 Z= 0.155 Angle : 0.637 9.727 18535 Z= 0.357 Chirality : 0.034 0.158 2099 Planarity : 0.004 0.055 1338 Dihedral : 30.085 144.629 4015 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.35 % Allowed : 33.65 % Favored : 63.00 % 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: 0.74 (0.30), residues: 749 helix: 1.17 (0.22), residues: 545 sheet: None (None), residues: 0 loop : -1.31 (0.38), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP E 47 HIS 0.005 0.001 HIS F 75 PHE 0.015 0.001 PHE F 100 TYR 0.054 0.003 TYR H 83 ARG 0.004 0.000 ARG G 29 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 745) hydrogen bonds : angle 3.01663 ( 1847) covalent geometry : bond 0.00334 (12810) covalent geometry : angle 0.63729 (18535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4170.85 seconds wall clock time: 77 minutes 46.50 seconds (4666.50 seconds total)