Starting phenix.real_space_refine on Sat Oct 12 12:34:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v26_42899/10_2024/8v26_42899_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v26_42899/10_2024/8v26_42899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v26_42899/10_2024/8v26_42899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v26_42899/10_2024/8v26_42899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v26_42899/10_2024/8v26_42899_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v26_42899/10_2024/8v26_42899_neut.cif" } resolution = 3.33 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 16 5.16 5 C 7063 2.51 5 N 2387 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 12689 Number of models: 1 Model: "" Number of chains: 11 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: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 764 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N LEU K 73 " occ=0.95 ... (6 atoms not shown) pdb=" CD2 LEU K 73 " occ=0.95 residue: pdb=" N ARG K 74 " occ=0.77 ... (9 atoms not shown) pdb=" NH2 ARG K 74 " occ=0.77 residue: pdb=" N GLY K 75 " occ=0.75 ... (2 atoms not shown) pdb=" O GLY K 75 " occ=0.75 Time building chain proxies: 7.39, per 1000 atoms: 0.58 Number of scatterers: 12689 At special positions: 0 Unit cell: (100.88, 123.19, 119.31, 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 16 16.00 P 288 15.00 O 2935 8.00 N 2387 7.00 C 7063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 117 " - pdb=" SG CYS K 76 " distance=2.56 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.97 Conformation dependent library (CDL) restraints added in 981.3 milliseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1592 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 66.5% alpha, 4.4% beta 139 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 5.38 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.525A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.834A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.833A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.651A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.557A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.196A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.541A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.548A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.628A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 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 81 removed outlier: 3.665A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.567A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.517A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.568A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.786A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.572A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.512A 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 76 removed outlier: 4.230A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.918A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.502A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.520A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.723A 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 100 through 121 removed outlier: 3.591A pdb=" N ALA H 121 " --> pdb=" O CYS H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 35 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.170A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.389A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.797A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.510A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.357A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16 removed outlier: 4.011A pdb=" N SER K 65 " --> pdb=" O GLN K 2 " (cutoff:3.500A) 415 hydrogen bonds defined for protein. 1233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 4.38 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2575 1.33 - 1.45: 4230 1.45 - 1.57: 6090 1.57 - 1.69: 576 1.69 - 1.81: 27 Bond restraints: 13498 Sorted by residual: bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.460 1.386 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 1.460 1.389 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" N ARG K 74 " pdb=" CA ARG K 74 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.27e-02 6.20e+03 6.40e+00 bond pdb=" C1' DT J -72 " pdb=" N1 DT J -72 " ideal model delta sigma weight residual 1.490 1.549 -0.059 3.00e-02 1.11e+03 3.86e+00 bond pdb=" C1' DT I -72 " pdb=" N1 DT I -72 " ideal model delta sigma weight residual 1.490 1.547 -0.057 3.00e-02 1.11e+03 3.62e+00 ... (remaining 13493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 19340 2.47 - 4.94: 109 4.94 - 7.41: 13 7.41 - 9.87: 2 9.87 - 12.34: 2 Bond angle restraints: 19466 Sorted by residual: angle pdb=" C3' DG I 71 " pdb=" O3' DG I 71 " pdb=" P DA I 72 " ideal model delta sigma weight residual 120.20 108.21 11.99 1.50e+00 4.44e-01 6.39e+01 angle pdb=" C3' DC I 70 " pdb=" O3' DC I 70 " pdb=" P DG I 71 " ideal model delta sigma weight residual 120.20 111.30 8.90 1.50e+00 4.44e-01 3.52e+01 angle pdb=" CA GLY K 75 " pdb=" C GLY K 75 " pdb=" O GLY K 75 " ideal model delta sigma weight residual 120.91 117.90 3.01 6.90e-01 2.10e+00 1.90e+01 angle pdb=" C3' DG J 71 " pdb=" O3' DG J 71 " pdb=" P DA J 72 " ideal model delta sigma weight residual 120.20 113.88 6.32 1.50e+00 4.44e-01 1.78e+01 angle pdb=" CB MET H 56 " pdb=" CG MET H 56 " pdb=" SD MET H 56 " ideal model delta sigma weight residual 112.70 100.36 12.34 3.00e+00 1.11e-01 1.69e+01 ... (remaining 19461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 6043 35.92 - 71.83: 1355 71.83 - 107.75: 8 107.75 - 143.67: 4 143.67 - 179.58: 1 Dihedral angle restraints: 7411 sinusoidal: 4948 harmonic: 2463 Sorted by residual: dihedral pdb=" CB CYS D 117 " pdb=" SG CYS D 117 " pdb=" SG CYS K 76 " pdb=" CB CYS K 76 " ideal model delta sinusoidal sigma weight residual 93.00 20.45 72.55 1 1.00e+01 1.00e-02 6.72e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 40.42 179.58 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 100.64 119.36 1 3.50e+01 8.16e-04 1.17e+01 ... (remaining 7408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2168 0.096 - 0.191: 47 0.191 - 0.287: 0 0.287 - 0.383: 0 0.383 - 0.479: 4 Chirality restraints: 2219 Sorted by residual: chirality pdb=" P DG J 71 " pdb=" OP1 DG J 71 " pdb=" OP2 DG J 71 " pdb=" O5' DG J 71 " both_signs ideal model delta sigma weight residual True 2.35 -2.82 -0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" P DG I 71 " pdb=" OP1 DG I 71 " pdb=" OP2 DG I 71 " pdb=" O5' DG I 71 " both_signs ideal model delta sigma weight residual True 2.35 -2.81 -0.46 2.00e-01 2.50e+01 5.34e+00 chirality pdb=" P DA J 72 " pdb=" OP1 DA J 72 " pdb=" OP2 DA J 72 " pdb=" O5' DA J 72 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.23e+00 ... (remaining 2216 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP F 24 " 0.011 2.00e-02 2.50e+03 2.22e-02 4.94e+00 pdb=" CG ASP F 24 " -0.038 2.00e-02 2.50e+03 pdb=" OD1 ASP F 24 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP F 24 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.59e+00 pdb=" C ASP F 24 " -0.037 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.014 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 24 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.92e+00 pdb=" CG ASP B 24 " 0.034 2.00e-02 2.50e+03 pdb=" OD1 ASP B 24 " -0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 24 " -0.012 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2181 2.78 - 3.31: 10455 3.31 - 3.84: 22518 3.84 - 4.37: 26520 4.37 - 4.90: 38861 Nonbonded interactions: 100535 Sorted by model distance: nonbonded pdb=" OE1 GLN K 40 " pdb=" NE2 GLN K 41 " model vdw 2.255 3.120 nonbonded pdb=" NH1 ARG K 42 " pdb=" OE1 GLN K 49 " model vdw 2.259 3.120 nonbonded pdb=" O THR E 58 " pdb=" OG1 THR E 58 " model vdw 2.275 3.040 nonbonded pdb=" N MET K 1 " pdb=" O VAL K 17 " model vdw 2.278 3.120 nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.320 3.120 ... (remaining 100530 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 121) 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=0.59 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.100 Process input model: 32.330 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 13498 Z= 0.209 Angle : 0.604 12.343 19466 Z= 0.364 Chirality : 0.039 0.479 2219 Planarity : 0.004 0.038 1463 Dihedral : 27.205 179.584 5816 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.28 % Allowed : 20.76 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.29), residues: 831 helix: 3.00 (0.22), residues: 525 sheet: -0.73 (0.98), residues: 26 loop : -1.31 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.008 0.001 PHE H 67 TYR 0.013 0.001 TYR H 39 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.026 Fit side-chains REVERT: K 6 LYS cc_start: 0.9172 (pttt) cc_final: 0.8944 (tptp) REVERT: K 68 HIS cc_start: 0.8962 (m170) cc_final: 0.8598 (m90) outliers start: 2 outliers final: 1 residues processed: 126 average time/residue: 0.3752 time to fit residues: 61.9230 Evaluate side-chains 125 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 chunk 27 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13498 Z= 0.180 Angle : 0.522 4.969 19466 Z= 0.320 Chirality : 0.033 0.257 2219 Planarity : 0.004 0.036 1463 Dihedral : 29.190 179.127 4116 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.82 % Allowed : 20.06 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.78 (0.30), residues: 831 helix: 3.26 (0.22), residues: 541 sheet: -0.46 (0.98), residues: 26 loop : -1.13 (0.34), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS K 68 PHE 0.009 0.001 PHE H 67 TYR 0.007 0.001 TYR H 37 ARG 0.006 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 131 time to evaluate : 0.826 Fit side-chains REVERT: K 1 MET cc_start: 0.6668 (pmm) cc_final: 0.6213 (pmm) outliers start: 13 outliers final: 8 residues processed: 136 average time/residue: 0.3444 time to fit residues: 62.2710 Evaluate side-chains 132 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 0.0970 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 20.0000 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8814 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 13498 Z= 0.392 Angle : 0.619 6.790 19466 Z= 0.371 Chirality : 0.039 0.152 2219 Planarity : 0.005 0.036 1463 Dihedral : 29.457 178.786 4116 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 3.09 % Allowed : 20.48 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.29), residues: 831 helix: 2.97 (0.22), residues: 540 sheet: -0.55 (0.93), residues: 26 loop : -1.31 (0.34), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 31 PHE 0.014 0.002 PHE D 67 TYR 0.016 0.002 TYR E 54 ARG 0.007 0.001 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 0.996 Fit side-chains REVERT: A 59 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8587 (pm20) REVERT: B 79 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8831 (mtmt) REVERT: F 92 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8195 (ttp80) REVERT: H 31 LYS cc_start: 0.8954 (mmtp) cc_final: 0.8475 (mtpt) outliers start: 22 outliers final: 15 residues processed: 133 average time/residue: 0.3648 time to fit residues: 63.1173 Evaluate side-chains 138 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 36 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 44 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 0.0470 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13498 Z= 0.170 Angle : 0.512 5.076 19466 Z= 0.313 Chirality : 0.033 0.129 2219 Planarity : 0.004 0.037 1463 Dihedral : 29.354 179.157 4116 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.38 % Allowed : 21.18 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.30), residues: 831 helix: 3.36 (0.22), residues: 542 sheet: -0.45 (1.00), residues: 26 loop : -1.17 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS K 68 PHE 0.009 0.001 PHE H 67 TYR 0.007 0.001 TYR G 50 ARG 0.006 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.783 Fit side-chains REVERT: A 59 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8489 (pm20) REVERT: A 63 ARG cc_start: 0.8604 (OUTLIER) cc_final: 0.8051 (mmp80) REVERT: G 95 LYS cc_start: 0.9331 (ttmm) cc_final: 0.9130 (ttmt) REVERT: H 31 LYS cc_start: 0.8923 (mmtp) cc_final: 0.8414 (mtpt) outliers start: 17 outliers final: 10 residues processed: 139 average time/residue: 0.3514 time to fit residues: 63.5249 Evaluate side-chains 136 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 68 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 86 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13498 Z= 0.243 Angle : 0.541 5.640 19466 Z= 0.328 Chirality : 0.034 0.151 2219 Planarity : 0.004 0.035 1463 Dihedral : 29.460 179.611 4114 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.81 % Allowed : 21.88 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.80 (0.30), residues: 831 helix: 3.34 (0.22), residues: 540 sheet: -0.59 (0.93), residues: 26 loop : -1.25 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 31 PHE 0.010 0.002 PHE H 67 TYR 0.008 0.001 TYR A 54 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 1.099 Fit side-chains REVERT: A 59 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8544 (pm20) REVERT: A 63 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8199 (mmp80) REVERT: H 28 LYS cc_start: 0.8446 (mtmm) cc_final: 0.8093 (pttm) REVERT: H 31 LYS cc_start: 0.8965 (mmtp) cc_final: 0.8472 (mtpt) REVERT: K 1 MET cc_start: 0.6653 (pmm) cc_final: 0.6244 (pmm) REVERT: K 42 ARG cc_start: 0.8193 (ttp80) cc_final: 0.7477 (ttp80) outliers start: 20 outliers final: 14 residues processed: 138 average time/residue: 0.3691 time to fit residues: 66.4452 Evaluate side-chains 140 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 124 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 68 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 10.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13498 Z= 0.198 Angle : 0.520 5.413 19466 Z= 0.317 Chirality : 0.033 0.159 2219 Planarity : 0.004 0.035 1463 Dihedral : 29.407 179.063 4114 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.52 % Allowed : 22.30 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.30), residues: 831 helix: 3.39 (0.22), residues: 540 sheet: -0.36 (1.00), residues: 26 loop : -1.23 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS K 68 PHE 0.009 0.001 PHE H 67 TYR 0.007 0.001 TYR A 54 ARG 0.008 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8475 (pm20) REVERT: A 63 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8140 (mmp80) REVERT: H 31 LYS cc_start: 0.8957 (mmtp) cc_final: 0.8465 (mtpt) REVERT: K 42 ARG cc_start: 0.8157 (ttp80) cc_final: 0.7379 (ttp80) outliers start: 18 outliers final: 15 residues processed: 136 average time/residue: 0.3619 time to fit residues: 64.1825 Evaluate side-chains 141 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain K residue 68 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 76 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 0.6980 chunk 104 optimal weight: 6.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 chunk 48 optimal weight: 0.0980 chunk 64 optimal weight: 6.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13498 Z= 0.158 Angle : 0.515 7.444 19466 Z= 0.312 Chirality : 0.032 0.163 2219 Planarity : 0.004 0.035 1463 Dihedral : 29.405 178.633 4114 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.38 % Allowed : 22.30 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.30), residues: 831 helix: 3.46 (0.22), residues: 540 sheet: -0.34 (0.96), residues: 26 loop : -1.19 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE H 67 TYR 0.008 0.001 TYR H 37 ARG 0.007 0.000 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.966 Fit side-chains REVERT: A 59 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8468 (pm20) REVERT: A 63 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8072 (mmp80) REVERT: H 31 LYS cc_start: 0.8960 (mmtp) cc_final: 0.8453 (mtpt) outliers start: 17 outliers final: 13 residues processed: 137 average time/residue: 0.3572 time to fit residues: 63.9971 Evaluate side-chains 141 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 126 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 68 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13498 Z= 0.245 Angle : 0.543 5.389 19466 Z= 0.328 Chirality : 0.034 0.156 2219 Planarity : 0.004 0.035 1463 Dihedral : 29.464 179.772 4114 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.38 % Allowed : 22.44 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.81 (0.30), residues: 831 helix: 3.36 (0.22), residues: 539 sheet: -0.43 (0.97), residues: 26 loop : -1.26 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 68 PHE 0.010 0.002 PHE B 61 TYR 0.009 0.001 TYR A 54 ARG 0.009 0.000 ARG K 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8541 (pm20) REVERT: A 63 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8167 (mmp80) REVERT: H 31 LYS cc_start: 0.8975 (mmtp) cc_final: 0.8483 (mtpt) outliers start: 17 outliers final: 14 residues processed: 138 average time/residue: 0.3644 time to fit residues: 65.2575 Evaluate side-chains 144 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 42 ARG Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain K residue 68 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 87 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 13498 Z= 0.401 Angle : 0.628 6.034 19466 Z= 0.375 Chirality : 0.039 0.177 2219 Planarity : 0.005 0.036 1463 Dihedral : 29.540 178.693 4114 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.52 % Allowed : 22.86 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.38 (0.29), residues: 831 helix: 3.01 (0.22), residues: 538 sheet: -0.58 (0.91), residues: 26 loop : -1.37 (0.34), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.016 0.002 PHE D 67 TYR 0.013 0.002 TYR A 54 ARG 0.009 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8552 (pm20) REVERT: A 63 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.8252 (mmp80) REVERT: D 31 LYS cc_start: 0.9260 (mtmm) cc_final: 0.9032 (mtmm) REVERT: H 31 LYS cc_start: 0.8971 (mmtp) cc_final: 0.8536 (mtpt) REVERT: K 42 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7957 (ttp80) outliers start: 18 outliers final: 15 residues processed: 136 average time/residue: 0.3807 time to fit residues: 67.3985 Evaluate side-chains 141 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 63 LYS Chi-restraints excluded: chain K residue 68 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 50.0000 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 30.0000 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13498 Z= 0.175 Angle : 0.524 6.847 19466 Z= 0.317 Chirality : 0.033 0.157 2219 Planarity : 0.004 0.037 1463 Dihedral : 29.428 179.077 4114 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.96 % Allowed : 23.42 % Favored : 74.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.30), residues: 831 helix: 3.40 (0.22), residues: 542 sheet: -0.53 (0.96), residues: 26 loop : -1.22 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE H 67 TYR 0.006 0.001 TYR F 51 ARG 0.009 0.000 ARG K 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8475 (pm20) REVERT: A 63 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8052 (mmp80) REVERT: H 31 LYS cc_start: 0.8978 (mmtp) cc_final: 0.8461 (mtpt) REVERT: K 42 ARG cc_start: 0.8280 (ttp80) cc_final: 0.7893 (ttp80) outliers start: 14 outliers final: 10 residues processed: 137 average time/residue: 0.3594 time to fit residues: 64.3614 Evaluate side-chains 137 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 3 ILE Chi-restraints excluded: chain K residue 44 ILE Chi-restraints excluded: chain K residue 68 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 6.9990 chunk 26 optimal weight: 0.0970 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 0.0020 chunk 88 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.2328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.094341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.062795 restraints weight = 28663.472| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.12 r_work: 0.2688 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.59 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13498 Z= 0.196 Angle : 0.536 6.431 19466 Z= 0.322 Chirality : 0.033 0.156 2219 Planarity : 0.004 0.035 1463 Dihedral : 29.490 179.233 4114 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.82 % Allowed : 23.70 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.30), residues: 831 helix: 3.46 (0.22), residues: 540 sheet: -0.75 (0.98), residues: 27 loop : -1.19 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 68 PHE 0.009 0.001 PHE H 67 TYR 0.008 0.001 TYR A 54 ARG 0.008 0.000 ARG K 42 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: