Starting phenix.real_space_refine on Tue Nov 18 06:06:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6esf_3947/11_2025/6esf_3947.cif Found real_map, /net/cci-nas-00/data/ceres_data/6esf_3947/11_2025/6esf_3947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6esf_3947/11_2025/6esf_3947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6esf_3947/11_2025/6esf_3947.map" model { file = "/net/cci-nas-00/data/ceres_data/6esf_3947/11_2025/6esf_3947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6esf_3947/11_2025/6esf_3947.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.011 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 294 5.49 5 S 12 5.16 5 C 6680 2.51 5 N 2275 2.21 5 O 2830 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12091 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 678 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 804 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "F" Number of atoms: 683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 683 Classifications: {'peptide': 85} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "G" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 811 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Time building chain proxies: 3.22, per 1000 atoms: 0.27 Number of scatterers: 12091 At special positions: 0 Unit cell: (82.96, 121.04, 114.24, 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 12 16.00 P 294 15.00 O 2830 8.00 N 2275 7.00 C 6680 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: 1.07 Conformation dependent library (CDL) restraints added in 440.2 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1430 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 68.9% alpha, 2.4% beta 142 base pairs and 246 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.087A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.546A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.663A 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: 3.606A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR B 72 " --> pdb=" O ASP B 68 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.681A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.546A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 79 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.746A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.600A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.549A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.697A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.697A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS F 75 " --> pdb=" O THR F 71 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.863A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 72 Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.518A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 4.309A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.603A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.061A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.677A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 101 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.780A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.766A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 374 hydrogen bonds defined for protein. 1116 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 363 hydrogen bonds 722 hydrogen bond angles 0 basepair planarities 142 basepair parallelities 246 stacking parallelities Total time for adding SS restraints: 2.58 Time building geometry restraints manager: 1.47 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: 1923 1.33 - 1.45: 4420 1.45 - 1.56: 5955 1.56 - 1.68: 586 1.68 - 1.80: 22 Bond restraints: 12906 Sorted by residual: bond pdb=" CB ASP A 106 " pdb=" CG ASP A 106 " ideal model delta sigma weight residual 1.516 1.478 0.038 2.50e-02 1.60e+03 2.37e+00 bond pdb=" C3' DC J 6 " pdb=" O3' DC J 6 " ideal model delta sigma weight residual 1.422 1.376 0.046 3.00e-02 1.11e+03 2.36e+00 bond pdb=" C3' DC I 52 " pdb=" O3' DC I 52 " ideal model delta sigma weight residual 1.422 1.468 -0.046 3.00e-02 1.11e+03 2.31e+00 bond pdb=" C1' DT I 9 " pdb=" N1 DT I 9 " ideal model delta sigma weight residual 1.490 1.446 0.044 3.00e-02 1.11e+03 2.19e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.465 -0.043 3.00e-02 1.11e+03 2.06e+00 ... (remaining 12901 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 17351 1.83 - 3.66: 1211 3.66 - 5.49: 103 5.49 - 7.32: 22 7.32 - 9.14: 5 Bond angle restraints: 18692 Sorted by residual: angle pdb=" C GLN G 84 " pdb=" N LEU G 85 " pdb=" CA LEU G 85 " ideal model delta sigma weight residual 121.58 115.18 6.40 1.95e+00 2.63e-01 1.08e+01 angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DG I 21 " ideal model delta sigma weight residual 120.20 125.05 -4.85 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C GLN C 84 " pdb=" N LEU C 85 " pdb=" CA LEU C 85 " ideal model delta sigma weight residual 121.14 115.58 5.56 1.75e+00 3.27e-01 1.01e+01 angle pdb=" C ALA C 60 " pdb=" N GLU C 61 " pdb=" CA GLU C 61 " ideal model delta sigma weight residual 121.14 115.59 5.55 1.75e+00 3.27e-01 1.01e+01 angle pdb=" C3' DT I -59 " pdb=" C2' DT I -59 " pdb=" C1' DT I -59 " ideal model delta sigma weight residual 101.60 97.03 4.57 1.50e+00 4.44e-01 9.27e+00 ... (remaining 18687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 5499 35.90 - 71.80: 1480 71.80 - 107.69: 27 107.69 - 143.59: 1 143.59 - 179.49: 1 Dihedral angle restraints: 7008 sinusoidal: 4794 harmonic: 2214 Sorted by residual: dihedral pdb=" CA LEU E 60 " pdb=" C LEU E 60 " pdb=" N LEU E 61 " pdb=" CA LEU E 61 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA TYR H 34 " pdb=" C TYR H 34 " pdb=" N ALA H 35 " pdb=" CA ALA H 35 " ideal model delta harmonic sigma weight residual 180.00 -155.97 -24.03 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA ILE A 62 " pdb=" C ILE A 62 " pdb=" N ARG A 63 " pdb=" CA ARG A 63 " ideal model delta harmonic sigma weight residual 180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 ... (remaining 7005 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1518 0.053 - 0.106: 514 0.106 - 0.158: 90 0.158 - 0.211: 7 0.211 - 0.264: 1 Chirality restraints: 2130 Sorted by residual: chirality pdb=" CG LEU G 34 " pdb=" CB LEU G 34 " pdb=" CD1 LEU G 34 " pdb=" CD2 LEU G 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CG LEU C 34 " pdb=" CB LEU C 34 " pdb=" CD1 LEU C 34 " pdb=" CD2 LEU C 34 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2127 not shown) Planarity restraints: 1345 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU D 99 " -0.042 5.00e-02 4.00e+02 6.33e-02 6.42e+00 pdb=" N PRO D 100 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO D 100 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 100 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 67 " 0.033 2.00e-02 2.50e+03 1.59e-02 6.32e+00 pdb=" N1 DT I 67 " -0.034 2.00e-02 2.50e+03 pdb=" C2 DT I 67 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 67 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DT I 67 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 67 " 0.009 2.00e-02 2.50e+03 pdb=" O4 DT I 67 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 67 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 67 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 67 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 26 " -0.035 2.00e-02 2.50e+03 1.46e-02 5.86e+00 pdb=" N9 DA I 26 " 0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 26 " 0.017 2.00e-02 2.50e+03 pdb=" N7 DA I 26 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 26 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA I 26 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 26 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DA I 26 " -0.000 2.00e-02 2.50e+03 pdb=" C2 DA I 26 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 26 " 0.011 2.00e-02 2.50e+03 pdb=" C4 DA I 26 " 0.005 2.00e-02 2.50e+03 ... (remaining 1342 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2465 2.78 - 3.31: 10427 3.31 - 3.84: 25095 3.84 - 4.37: 27796 4.37 - 4.90: 38509 Nonbonded interactions: 104292 Sorted by model distance: nonbonded pdb=" N2 DG I 73 " pdb=" O2 DC J -73 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE2 GLU A 133 " model vdw 2.275 3.040 nonbonded pdb=" OH TYR C 39 " pdb=" OE1 GLU D 68 " model vdw 2.282 3.040 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.293 3.040 nonbonded pdb=" O VAL H 115 " pdb=" OG1 THR H 119 " model vdw 2.299 3.040 ... (remaining 104287 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' and ((resid 37 and (name N or name CA or name C or name O or name CB \ )) or resid 38 through 134)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 18 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 16 through 119) } ncs_group { reference = chain 'D' 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: 0.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.490 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 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 : 0.008 0.070 12906 Z= 0.353 Angle : 0.973 9.144 18692 Z= 0.554 Chirality : 0.052 0.264 2130 Planarity : 0.007 0.063 1345 Dihedral : 28.705 179.491 5578 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 0.94 % Allowed : 3.13 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.25 (0.23), residues: 746 helix: -2.79 (0.15), residues: 510 sheet: None (None), residues: 0 loop : -2.41 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 129 TYR 0.016 0.003 TYR C 50 PHE 0.033 0.004 PHE C 25 HIS 0.014 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00797 (12906) covalent geometry : angle 0.97312 (18692) hydrogen bonds : bond 0.10461 ( 737) hydrogen bonds : angle 6.86556 ( 1838) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 282 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.7714 (mmtp) cc_final: 0.7458 (mttm) REVERT: A 123 ASP cc_start: 0.7701 (m-30) cc_final: 0.7457 (m-30) REVERT: C 33 LEU cc_start: 0.8327 (mt) cc_final: 0.7741 (tp) REVERT: C 76 THR cc_start: 0.8924 (p) cc_final: 0.8424 (t) REVERT: D 31 LYS cc_start: 0.7801 (mttt) cc_final: 0.7414 (pttm) REVERT: E 74 ILE cc_start: 0.8944 (mt) cc_final: 0.8636 (mt) REVERT: E 123 ASP cc_start: 0.7765 (m-30) cc_final: 0.7221 (m-30) REVERT: G 33 LEU cc_start: 0.8240 (mt) cc_final: 0.7816 (tp) REVERT: G 34 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8668 (mt) REVERT: G 84 GLN cc_start: 0.8332 (tp40) cc_final: 0.8090 (tp-100) REVERT: G 95 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7804 (tppt) REVERT: H 31 LYS cc_start: 0.8535 (tptp) cc_final: 0.8096 (ttpt) REVERT: H 48 ASP cc_start: 0.8133 (m-30) cc_final: 0.7677 (p0) REVERT: H 90 GLU cc_start: 0.7876 (mp0) cc_final: 0.7655 (mp0) REVERT: H 117 LYS cc_start: 0.8643 (tttm) cc_final: 0.8380 (tttt) outliers start: 6 outliers final: 1 residues processed: 286 average time/residue: 0.1443 time to fit residues: 55.2982 Evaluate side-chains 168 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.0070 chunk 45 optimal weight: 0.7980 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN C 24 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 38 ASN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.095467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080297 restraints weight = 43721.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.082077 restraints weight = 22015.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.083264 restraints weight = 14186.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.084023 restraints weight = 10912.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.084484 restraints weight = 9366.636| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12906 Z= 0.176 Angle : 0.655 10.781 18692 Z= 0.382 Chirality : 0.037 0.172 2130 Planarity : 0.006 0.057 1345 Dihedral : 32.236 178.888 4065 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.23 % Allowed : 14.26 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.28), residues: 746 helix: -0.15 (0.20), residues: 528 sheet: None (None), residues: 0 loop : -2.00 (0.41), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 77 TYR 0.023 0.002 TYR B 88 PHE 0.011 0.001 PHE E 104 HIS 0.012 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00375 (12906) covalent geometry : angle 0.65498 (18692) hydrogen bonds : bond 0.04950 ( 737) hydrogen bonds : angle 3.55882 ( 1838) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 208 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8002 (mm) cc_final: 0.7667 (mm) REVERT: A 94 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 123 ASP cc_start: 0.7865 (m-30) cc_final: 0.7391 (m-30) REVERT: C 25 PHE cc_start: 0.8894 (OUTLIER) cc_final: 0.8680 (m-80) REVERT: C 33 LEU cc_start: 0.8141 (mt) cc_final: 0.7895 (tp) REVERT: C 64 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7403 (tm-30) REVERT: C 76 THR cc_start: 0.8937 (p) cc_final: 0.8569 (t) REVERT: C 85 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7408 (mt) REVERT: C 95 LYS cc_start: 0.8520 (tppt) cc_final: 0.8315 (tptt) REVERT: C 100 VAL cc_start: 0.9205 (OUTLIER) cc_final: 0.8769 (m) REVERT: D 31 LYS cc_start: 0.7691 (mttt) cc_final: 0.7223 (pttt) REVERT: D 43 LYS cc_start: 0.7324 (mtpt) cc_final: 0.7112 (mtmt) REVERT: E 123 ASP cc_start: 0.8132 (m-30) cc_final: 0.7465 (m-30) REVERT: G 33 LEU cc_start: 0.8140 (mt) cc_final: 0.7803 (tp) REVERT: G 68 ASN cc_start: 0.8619 (t0) cc_final: 0.7844 (t0) REVERT: H 31 LYS cc_start: 0.8211 (tptp) cc_final: 0.7825 (ttpt) REVERT: H 110 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7756 (mm-30) REVERT: H 117 LYS cc_start: 0.8441 (tttm) cc_final: 0.8162 (ttpt) outliers start: 27 outliers final: 16 residues processed: 227 average time/residue: 0.1083 time to fit residues: 35.6072 Evaluate side-chains 182 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 25 PHE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 2 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 77 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.094018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.078408 restraints weight = 44091.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080119 restraints weight = 22789.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081237 restraints weight = 15087.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.081951 restraints weight = 11815.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.082357 restraints weight = 10273.844| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 12906 Z= 0.214 Angle : 0.665 8.733 18692 Z= 0.385 Chirality : 0.037 0.161 2130 Planarity : 0.005 0.053 1345 Dihedral : 32.106 179.916 4065 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 6.11 % Allowed : 17.24 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.30), residues: 746 helix: 0.89 (0.22), residues: 527 sheet: None (None), residues: 0 loop : -1.81 (0.43), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 77 TYR 0.013 0.002 TYR G 57 PHE 0.010 0.002 PHE F 100 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00472 (12906) covalent geometry : angle 0.66467 (18692) hydrogen bonds : bond 0.05225 ( 737) hydrogen bonds : angle 3.39859 ( 1838) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 160 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.7891 (m-30) cc_final: 0.7448 (m-30) REVERT: B 49 LEU cc_start: 0.8715 (mp) cc_final: 0.8486 (mp) REVERT: B 74 GLU cc_start: 0.8138 (tp30) cc_final: 0.7484 (tp30) REVERT: C 33 LEU cc_start: 0.8464 (mt) cc_final: 0.8032 (tp) REVERT: C 64 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7456 (tm-30) REVERT: C 76 THR cc_start: 0.8931 (p) cc_final: 0.8690 (t) REVERT: D 31 LYS cc_start: 0.7712 (mttt) cc_final: 0.7296 (pttt) REVERT: D 36 ILE cc_start: 0.8388 (OUTLIER) cc_final: 0.8149 (mt) REVERT: D 59 MET cc_start: 0.8370 (tpp) cc_final: 0.7784 (tpp) REVERT: D 117 LYS cc_start: 0.8245 (tttt) cc_final: 0.7540 (tttt) REVERT: E 123 ASP cc_start: 0.8141 (m-30) cc_final: 0.7262 (m-30) REVERT: G 33 LEU cc_start: 0.8259 (mt) cc_final: 0.7898 (tp) REVERT: G 68 ASN cc_start: 0.8640 (t0) cc_final: 0.7810 (t0) REVERT: H 31 LYS cc_start: 0.8214 (tptp) cc_final: 0.7690 (ttpt) REVERT: H 34 TYR cc_start: 0.8408 (m-80) cc_final: 0.7937 (m-10) REVERT: H 40 LYS cc_start: 0.8899 (mttt) cc_final: 0.8635 (mttm) REVERT: H 43 LYS cc_start: 0.8314 (mttt) cc_final: 0.8058 (mptt) REVERT: H 48 ASP cc_start: 0.7707 (p0) cc_final: 0.7367 (p0) REVERT: H 110 GLU cc_start: 0.7874 (mm-30) cc_final: 0.7555 (mm-30) outliers start: 39 outliers final: 28 residues processed: 191 average time/residue: 0.1001 time to fit residues: 28.6937 Evaluate side-chains 179 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 75 optimal weight: 8.9990 chunk 21 optimal weight: 3.9990 chunk 79 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 96 optimal weight: 10.0000 chunk 92 optimal weight: 8.9990 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** H 81 ASN ** 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 = 0.3707 r_free = 0.3707 target = 0.093483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.077178 restraints weight = 43700.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.078805 restraints weight = 23070.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079894 restraints weight = 15568.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.080536 restraints weight = 12345.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.080944 restraints weight = 10851.053| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12906 Z= 0.264 Angle : 0.700 7.694 18692 Z= 0.403 Chirality : 0.039 0.153 2130 Planarity : 0.006 0.051 1345 Dihedral : 32.107 179.007 4063 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 5.64 % Allowed : 19.59 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.31), residues: 746 helix: 1.01 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.78 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 77 TYR 0.018 0.002 TYR F 88 PHE 0.011 0.002 PHE C 25 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00585 (12906) covalent geometry : angle 0.70032 (18692) hydrogen bonds : bond 0.05755 ( 737) hydrogen bonds : angle 3.59574 ( 1838) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 149 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7340 (t70) cc_final: 0.7134 (t70) REVERT: A 108 ASN cc_start: 0.8392 (t0) cc_final: 0.7933 (t0) REVERT: A 123 ASP cc_start: 0.8022 (m-30) cc_final: 0.7626 (m-30) REVERT: B 74 GLU cc_start: 0.8202 (tp30) cc_final: 0.7521 (tp30) REVERT: C 33 LEU cc_start: 0.8464 (mt) cc_final: 0.8031 (tp) REVERT: C 64 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7499 (tm-30) REVERT: C 76 THR cc_start: 0.8958 (p) cc_final: 0.8742 (t) REVERT: D 31 LYS cc_start: 0.7832 (mttt) cc_final: 0.7346 (pttt) REVERT: D 36 ILE cc_start: 0.8462 (OUTLIER) cc_final: 0.8246 (mt) REVERT: D 59 MET cc_start: 0.8414 (tpp) cc_final: 0.7739 (tpp) REVERT: D 90 GLU cc_start: 0.8062 (mp0) cc_final: 0.7777 (pm20) REVERT: E 123 ASP cc_start: 0.8173 (m-30) cc_final: 0.7326 (m-30) REVERT: G 33 LEU cc_start: 0.8358 (mt) cc_final: 0.8091 (tp) REVERT: G 68 ASN cc_start: 0.8720 (t0) cc_final: 0.8116 (t0) REVERT: H 31 LYS cc_start: 0.8145 (tptp) cc_final: 0.7694 (ttpt) REVERT: H 39 TYR cc_start: 0.7760 (t80) cc_final: 0.7499 (t80) REVERT: H 48 ASP cc_start: 0.7754 (p0) cc_final: 0.7287 (p0) REVERT: H 59 MET cc_start: 0.8361 (tpp) cc_final: 0.8158 (mmm) REVERT: H 110 GLU cc_start: 0.7855 (mm-30) cc_final: 0.7532 (mm-30) outliers start: 36 outliers final: 29 residues processed: 175 average time/residue: 0.0930 time to fit residues: 24.7657 Evaluate side-chains 171 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 89 optimal weight: 8.9990 chunk 61 optimal weight: 0.9990 chunk 51 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** 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 = 0.3738 r_free = 0.3738 target = 0.095037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.078656 restraints weight = 43260.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.080365 restraints weight = 22501.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.081502 restraints weight = 14946.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.082156 restraints weight = 11734.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.082575 restraints weight = 10278.083| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12906 Z= 0.192 Angle : 0.633 8.734 18692 Z= 0.367 Chirality : 0.036 0.156 2130 Planarity : 0.005 0.051 1345 Dihedral : 31.928 177.839 4063 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.96 % Allowed : 20.06 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.31), residues: 746 helix: 1.44 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.71 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 77 TYR 0.018 0.002 TYR F 88 PHE 0.008 0.001 PHE D 67 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00423 (12906) covalent geometry : angle 0.63316 (18692) hydrogen bonds : bond 0.04835 ( 737) hydrogen bonds : angle 3.23249 ( 1838) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 155 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.7284 (t70) cc_final: 0.6944 (t70) REVERT: A 108 ASN cc_start: 0.8344 (t0) cc_final: 0.8074 (t0) REVERT: A 123 ASP cc_start: 0.7883 (m-30) cc_final: 0.7114 (m-30) REVERT: B 74 GLU cc_start: 0.8202 (tp30) cc_final: 0.7455 (tp30) REVERT: B 84 MET cc_start: 0.7797 (tpp) cc_final: 0.7512 (tpp) REVERT: C 33 LEU cc_start: 0.8424 (mt) cc_final: 0.8071 (tp) REVERT: C 61 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7351 (tp30) REVERT: C 76 THR cc_start: 0.8872 (p) cc_final: 0.8613 (t) REVERT: D 31 LYS cc_start: 0.7546 (mttt) cc_final: 0.7166 (pttt) REVERT: D 59 MET cc_start: 0.8354 (tpp) cc_final: 0.7641 (tpp) REVERT: D 90 GLU cc_start: 0.7983 (mp0) cc_final: 0.7625 (mp0) REVERT: D 117 LYS cc_start: 0.8189 (tttt) cc_final: 0.7565 (tttt) REVERT: E 123 ASP cc_start: 0.8170 (m-30) cc_final: 0.7461 (m-30) REVERT: G 33 LEU cc_start: 0.8354 (mt) cc_final: 0.8137 (tp) REVERT: G 68 ASN cc_start: 0.8781 (t0) cc_final: 0.8104 (t0) REVERT: H 31 LYS cc_start: 0.8045 (tptp) cc_final: 0.7630 (ttpt) REVERT: H 34 TYR cc_start: 0.8521 (m-80) cc_final: 0.8052 (m-10) REVERT: H 39 TYR cc_start: 0.7706 (t80) cc_final: 0.7466 (t80) REVERT: H 48 ASP cc_start: 0.7769 (p0) cc_final: 0.7301 (p0) REVERT: H 117 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8252 (ttpt) outliers start: 38 outliers final: 28 residues processed: 183 average time/residue: 0.0935 time to fit residues: 25.9327 Evaluate side-chains 173 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 145 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 40 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** E 108 ASN ** 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 = 0.3753 r_free = 0.3753 target = 0.095873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.079570 restraints weight = 43299.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.081326 restraints weight = 22283.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.082480 restraints weight = 14695.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.083157 restraints weight = 11493.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.083431 restraints weight = 10039.019| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12906 Z= 0.168 Angle : 0.621 9.058 18692 Z= 0.357 Chirality : 0.035 0.156 2130 Planarity : 0.005 0.053 1345 Dihedral : 31.793 178.210 4063 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 5.80 % Allowed : 21.47 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.31), residues: 746 helix: 1.68 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.52 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 83 TYR 0.018 0.002 TYR B 88 PHE 0.007 0.001 PHE D 67 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00367 (12906) covalent geometry : angle 0.62086 (18692) hydrogen bonds : bond 0.04524 ( 737) hydrogen bonds : angle 3.07384 ( 1838) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8038 (p) cc_final: 0.7712 (p) REVERT: A 123 ASP cc_start: 0.7889 (m-30) cc_final: 0.7104 (m-30) REVERT: B 74 GLU cc_start: 0.8127 (tp30) cc_final: 0.7344 (tp30) REVERT: C 33 LEU cc_start: 0.8392 (mt) cc_final: 0.8068 (tp) REVERT: C 56 GLU cc_start: 0.8462 (tt0) cc_final: 0.7969 (tm-30) REVERT: C 61 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7935 (tp30) REVERT: D 31 LYS cc_start: 0.7533 (mttt) cc_final: 0.7149 (pttt) REVERT: D 59 MET cc_start: 0.8307 (tpp) cc_final: 0.7579 (tpp) REVERT: D 90 GLU cc_start: 0.8075 (mp0) cc_final: 0.7736 (mp0) REVERT: D 117 LYS cc_start: 0.8063 (tttt) cc_final: 0.7723 (tptt) REVERT: E 87 SER cc_start: 0.7958 (p) cc_final: 0.7680 (p) REVERT: E 123 ASP cc_start: 0.7925 (m-30) cc_final: 0.6937 (m-30) REVERT: G 68 ASN cc_start: 0.8655 (t0) cc_final: 0.7936 (t0) REVERT: H 31 LYS cc_start: 0.7962 (tptp) cc_final: 0.7548 (ttpt) REVERT: H 34 TYR cc_start: 0.8486 (m-80) cc_final: 0.8000 (m-10) REVERT: H 39 TYR cc_start: 0.7733 (t80) cc_final: 0.7152 (t80) REVERT: H 43 LYS cc_start: 0.8354 (mttt) cc_final: 0.7941 (mptt) REVERT: H 48 ASP cc_start: 0.7768 (p0) cc_final: 0.7285 (p0) REVERT: H 59 MET cc_start: 0.8348 (tpp) cc_final: 0.7926 (tpp) outliers start: 37 outliers final: 28 residues processed: 186 average time/residue: 0.0922 time to fit residues: 26.1417 Evaluate side-chains 175 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 74 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 73 optimal weight: 10.0000 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** B 75 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 = 0.3755 r_free = 0.3755 target = 0.096091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.080292 restraints weight = 43436.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.082033 restraints weight = 22911.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.083165 restraints weight = 15252.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.083869 restraints weight = 11980.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.084224 restraints weight = 10442.923| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12906 Z= 0.162 Angle : 0.618 8.842 18692 Z= 0.353 Chirality : 0.035 0.157 2130 Planarity : 0.005 0.053 1345 Dihedral : 31.680 178.011 4063 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.17 % Allowed : 22.10 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.32), residues: 746 helix: 1.74 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.42 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 30 TYR 0.013 0.001 TYR G 39 PHE 0.007 0.001 PHE H 67 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00356 (12906) covalent geometry : angle 0.61790 (18692) hydrogen bonds : bond 0.04396 ( 737) hydrogen bonds : angle 3.01559 ( 1838) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 158 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7325 (m-80) cc_final: 0.6775 (m-80) REVERT: A 87 SER cc_start: 0.8129 (p) cc_final: 0.7794 (p) REVERT: A 106 ASP cc_start: 0.7162 (t70) cc_final: 0.6957 (t70) REVERT: A 123 ASP cc_start: 0.7765 (m-30) cc_final: 0.6950 (m-30) REVERT: C 33 LEU cc_start: 0.8361 (mt) cc_final: 0.8051 (tp) REVERT: C 61 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7841 (tp30) REVERT: D 31 LYS cc_start: 0.7404 (mttt) cc_final: 0.7178 (pttt) REVERT: D 59 MET cc_start: 0.8251 (tpp) cc_final: 0.7862 (tpp) REVERT: D 117 LYS cc_start: 0.7969 (tttt) cc_final: 0.7675 (tptt) REVERT: E 82 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8429 (mt) REVERT: E 87 SER cc_start: 0.7868 (p) cc_final: 0.7508 (p) REVERT: E 123 ASP cc_start: 0.7958 (m-30) cc_final: 0.7214 (m-30) REVERT: F 84 MET cc_start: 0.7515 (tpp) cc_final: 0.7190 (tpp) REVERT: G 68 ASN cc_start: 0.8591 (t0) cc_final: 0.7809 (t0) REVERT: H 31 LYS cc_start: 0.8090 (tptp) cc_final: 0.7661 (ttpt) REVERT: H 34 TYR cc_start: 0.8429 (m-80) cc_final: 0.7944 (m-10) REVERT: H 43 LYS cc_start: 0.8331 (mttt) cc_final: 0.7874 (mptt) REVERT: H 48 ASP cc_start: 0.7659 (p0) cc_final: 0.7149 (p0) REVERT: H 59 MET cc_start: 0.8303 (tpp) cc_final: 0.7655 (tpp) outliers start: 33 outliers final: 29 residues processed: 181 average time/residue: 0.0945 time to fit residues: 25.9870 Evaluate side-chains 176 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 146 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 59 optimal weight: 10.0000 chunk 35 optimal weight: 8.9990 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 48 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN ** B 75 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 = 0.3743 r_free = 0.3743 target = 0.095325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.078982 restraints weight = 43212.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.080663 restraints weight = 22477.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.081784 restraints weight = 14948.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.082466 restraints weight = 11771.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.082876 restraints weight = 10305.380| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12906 Z= 0.201 Angle : 0.650 8.925 18692 Z= 0.370 Chirality : 0.036 0.150 2130 Planarity : 0.005 0.052 1345 Dihedral : 31.684 178.167 4063 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.96 % Allowed : 22.41 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.31), residues: 746 helix: 1.69 (0.22), residues: 524 sheet: None (None), residues: 0 loop : -1.51 (0.43), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 77 TYR 0.015 0.002 TYR H 80 PHE 0.009 0.001 PHE D 67 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00445 (12906) covalent geometry : angle 0.64984 (18692) hydrogen bonds : bond 0.04906 ( 737) hydrogen bonds : angle 3.18509 ( 1838) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8051 (p) cc_final: 0.7742 (p) REVERT: A 106 ASP cc_start: 0.7207 (t70) cc_final: 0.6928 (t70) REVERT: A 123 ASP cc_start: 0.7881 (m-30) cc_final: 0.7259 (m-30) REVERT: C 33 LEU cc_start: 0.8438 (mt) cc_final: 0.8120 (tp) REVERT: C 61 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8047 (tp30) REVERT: D 31 LYS cc_start: 0.7533 (mttt) cc_final: 0.7204 (pttt) REVERT: D 59 MET cc_start: 0.8344 (tpp) cc_final: 0.7570 (tpp) REVERT: D 117 LYS cc_start: 0.8060 (tttt) cc_final: 0.7709 (tptt) REVERT: E 82 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8381 (mt) REVERT: E 123 ASP cc_start: 0.8093 (m-30) cc_final: 0.7854 (m-30) REVERT: G 68 ASN cc_start: 0.8617 (t0) cc_final: 0.7911 (t0) REVERT: H 31 LYS cc_start: 0.8146 (tptp) cc_final: 0.7683 (ttpt) REVERT: H 34 TYR cc_start: 0.8546 (m-80) cc_final: 0.7988 (m-10) REVERT: H 39 TYR cc_start: 0.7829 (t80) cc_final: 0.7243 (t80) REVERT: H 43 LYS cc_start: 0.8352 (mttt) cc_final: 0.7956 (mptt) REVERT: H 48 ASP cc_start: 0.7762 (p0) cc_final: 0.7215 (p0) REVERT: H 59 MET cc_start: 0.8571 (tpp) cc_final: 0.7891 (tpp) REVERT: H 86 ILE cc_start: 0.8483 (mt) cc_final: 0.8250 (mt) REVERT: H 90 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7277 (pm20) outliers start: 38 outliers final: 32 residues processed: 172 average time/residue: 0.0975 time to fit residues: 26.1138 Evaluate side-chains 176 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 63 VAL Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 0.0010 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 83 optimal weight: 8.9990 chunk 72 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** 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 = 0.3775 r_free = 0.3775 target = 0.097005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.080822 restraints weight = 42907.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.082563 restraints weight = 22137.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.083699 restraints weight = 14620.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.084422 restraints weight = 11468.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.084781 restraints weight = 9982.518| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12906 Z= 0.157 Angle : 0.629 9.562 18692 Z= 0.356 Chirality : 0.035 0.154 2130 Planarity : 0.004 0.054 1345 Dihedral : 31.596 177.858 4063 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.08 % Allowed : 23.98 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.31), residues: 746 helix: 1.83 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.46 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.016 0.002 TYR G 39 PHE 0.007 0.001 PHE H 67 HIS 0.005 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00346 (12906) covalent geometry : angle 0.62875 (18692) hydrogen bonds : bond 0.04298 ( 737) hydrogen bonds : angle 2.97963 ( 1838) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.7444 (m-80) cc_final: 0.6801 (m-80) REVERT: A 87 SER cc_start: 0.8014 (p) cc_final: 0.7715 (p) REVERT: A 108 ASN cc_start: 0.8048 (t0) cc_final: 0.7517 (t0) REVERT: C 33 LEU cc_start: 0.8389 (mt) cc_final: 0.8070 (tp) REVERT: C 56 GLU cc_start: 0.8420 (tt0) cc_final: 0.7905 (tm-30) REVERT: C 61 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8037 (tp30) REVERT: D 31 LYS cc_start: 0.7426 (mttt) cc_final: 0.7115 (pttt) REVERT: D 59 MET cc_start: 0.8339 (tpp) cc_final: 0.7940 (tpp) REVERT: D 117 LYS cc_start: 0.7923 (tttt) cc_final: 0.7647 (tptt) REVERT: E 73 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8405 (tm-30) REVERT: E 87 SER cc_start: 0.7851 (p) cc_final: 0.7435 (p) REVERT: E 123 ASP cc_start: 0.8005 (m-30) cc_final: 0.7115 (m-30) REVERT: G 68 ASN cc_start: 0.8540 (t0) cc_final: 0.7796 (t0) REVERT: H 31 LYS cc_start: 0.8166 (tptp) cc_final: 0.7583 (ttpt) REVERT: H 34 TYR cc_start: 0.8458 (m-80) cc_final: 0.7930 (m-10) REVERT: H 48 ASP cc_start: 0.7661 (p0) cc_final: 0.7141 (p0) REVERT: H 59 MET cc_start: 0.8407 (tpp) cc_final: 0.7737 (tpp) REVERT: H 86 ILE cc_start: 0.8434 (mt) cc_final: 0.8227 (mt) outliers start: 26 outliers final: 21 residues processed: 178 average time/residue: 0.0989 time to fit residues: 26.4432 Evaluate side-chains 169 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 47 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 85 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 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 = 0.3761 r_free = 0.3761 target = 0.096277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.079941 restraints weight = 43389.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.081666 restraints weight = 22410.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.082790 restraints weight = 14836.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.083494 restraints weight = 11650.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.083851 restraints weight = 10164.810| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12906 Z= 0.176 Angle : 0.666 10.531 18692 Z= 0.372 Chirality : 0.036 0.183 2130 Planarity : 0.006 0.114 1345 Dihedral : 31.567 177.994 4063 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.76 % Allowed : 24.61 % Favored : 71.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.31), residues: 746 helix: 1.70 (0.22), residues: 523 sheet: None (None), residues: 0 loop : -1.49 (0.43), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.015 0.002 TYR G 39 PHE 0.007 0.001 PHE H 67 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00391 (12906) covalent geometry : angle 0.66637 (18692) hydrogen bonds : bond 0.04576 ( 737) hydrogen bonds : angle 3.10536 ( 1838) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.8058 (p) cc_final: 0.7724 (p) REVERT: A 106 ASP cc_start: 0.7315 (t70) cc_final: 0.7007 (t70) REVERT: A 108 ASN cc_start: 0.7984 (t0) cc_final: 0.7499 (t0) REVERT: C 33 LEU cc_start: 0.8414 (mt) cc_final: 0.8099 (tp) REVERT: C 56 GLU cc_start: 0.8403 (tt0) cc_final: 0.7842 (tm-30) REVERT: C 61 GLU cc_start: 0.8370 (mm-30) cc_final: 0.8105 (tp30) REVERT: D 31 LYS cc_start: 0.7431 (mttt) cc_final: 0.7165 (pttt) REVERT: D 59 MET cc_start: 0.8386 (tpp) cc_final: 0.7970 (tpp) REVERT: D 117 LYS cc_start: 0.7992 (tttt) cc_final: 0.7747 (tptt) REVERT: E 79 LYS cc_start: 0.8028 (tmmt) cc_final: 0.7738 (ptmm) REVERT: E 87 SER cc_start: 0.8079 (p) cc_final: 0.7816 (p) REVERT: E 123 ASP cc_start: 0.7983 (m-30) cc_final: 0.7134 (m-30) REVERT: G 68 ASN cc_start: 0.8587 (t0) cc_final: 0.7787 (t0) REVERT: H 31 LYS cc_start: 0.8026 (tptp) cc_final: 0.7511 (ttpt) REVERT: H 59 MET cc_start: 0.8554 (tpp) cc_final: 0.7857 (tpp) outliers start: 24 outliers final: 23 residues processed: 170 average time/residue: 0.0993 time to fit residues: 25.5005 Evaluate side-chains 166 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 18 SER Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 58 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 77 LEU Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 77 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 64 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** F 75 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 = 0.3707 r_free = 0.3707 target = 0.093501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.077095 restraints weight = 43466.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.078730 restraints weight = 22679.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.079806 restraints weight = 15121.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.080455 restraints weight = 11946.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.080781 restraints weight = 10508.909| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 12906 Z= 0.280 Angle : 0.762 10.005 18692 Z= 0.426 Chirality : 0.040 0.180 2130 Planarity : 0.007 0.120 1345 Dihedral : 31.828 178.490 4063 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 4.55 % Allowed : 24.45 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.31), residues: 746 helix: 1.21 (0.22), residues: 521 sheet: None (None), residues: 0 loop : -1.67 (0.42), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 116 TYR 0.024 0.003 TYR H 80 PHE 0.012 0.002 PHE D 67 HIS 0.009 0.002 HIS A 113 Details of bonding type rmsd covalent geometry : bond 0.00627 (12906) covalent geometry : angle 0.76171 (18692) hydrogen bonds : bond 0.06074 ( 737) hydrogen bonds : angle 3.66931 ( 1838) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1768.67 seconds wall clock time: 31 minutes 20.66 seconds (1880.66 seconds total)