Starting phenix.real_space_refine on Thu Sep 26 06:28:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v25_42898/09_2024/8v25_42898_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v25_42898/09_2024/8v25_42898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v25_42898/09_2024/8v25_42898.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v25_42898/09_2024/8v25_42898.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v25_42898/09_2024/8v25_42898_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v25_42898/09_2024/8v25_42898_neut.cif" } resolution = 3.32 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 17 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 2 residue: pdb=" N ARG K 74 " occ=0.95 ... (9 atoms not shown) pdb=" NH2 ARG K 74 " occ=0.95 residue: pdb=" N GLY K 75 " occ=0.65 ... (2 atoms not shown) pdb=" O GLY K 75 " occ=0.65 Time building chain proxies: 7.40, per 1000 atoms: 0.58 Number of scatterers: 12689 At special positions: 0 Unit cell: (101.85, 122.22, 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=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: 3.31 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 37 helices and 9 sheets defined 66.9% alpha, 4.2% beta 138 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 6.18 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.520A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.803A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.860A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.622A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.099A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.656A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.649A 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 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: 3.588A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.558A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.599A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.607A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.533A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.190A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.543A 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: 3.506A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.520A 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: 3.611A 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 Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.109A 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: 7.324A 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: 6.895A 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 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.346A 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 16 421 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 4.77 Time building geometry restraints manager: 3.82 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: 2639 1.33 - 1.45: 4191 1.45 - 1.57: 6065 1.57 - 1.69: 576 1.69 - 1.81: 27 Bond restraints: 13498 Sorted by residual: 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=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.460 1.391 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N THR K 55 " pdb=" CA THR K 55 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.36e+00 bond pdb=" N ARG K 72 " pdb=" CA ARG K 72 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.24e-02 6.50e+03 5.94e+00 bond pdb=" N LEU K 56 " pdb=" CA LEU K 56 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.27e-02 6.20e+03 4.41e+00 ... (remaining 13493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 19259 2.27 - 4.53: 176 4.53 - 6.80: 27 6.80 - 9.06: 3 9.06 - 11.33: 1 Bond angle restraints: 19466 Sorted by residual: angle pdb=" C3' DG J 71 " pdb=" O3' DG J 71 " pdb=" P DA J 72 " ideal model delta sigma weight residual 120.20 108.87 11.33 1.50e+00 4.44e-01 5.71e+01 angle pdb=" C3' DG I 71 " pdb=" O3' DG I 71 " pdb=" P DA I 72 " ideal model delta sigma weight residual 120.20 112.34 7.86 1.50e+00 4.44e-01 2.74e+01 angle pdb=" C3' DC J 70 " pdb=" O3' DC J 70 " pdb=" P DG J 71 " ideal model delta sigma weight residual 120.20 113.10 7.10 1.50e+00 4.44e-01 2.24e+01 angle pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sigma weight residual 120.20 114.19 6.01 1.50e+00 4.44e-01 1.60e+01 angle pdb=" C ASP F 24 " pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 111.40 116.33 -4.93 1.29e+00 6.01e-01 1.46e+01 ... (remaining 19461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6017 35.81 - 71.62: 1378 71.62 - 107.44: 8 107.44 - 143.25: 4 143.25 - 179.06: 1 Dihedral angle restraints: 7408 sinusoidal: 4945 harmonic: 2463 Sorted by residual: dihedral pdb=" CA MET K 1 " pdb=" C MET K 1 " pdb=" N GLN K 2 " pdb=" CA GLN K 2 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+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 -140.00 39.06 -179.06 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 94.61 125.39 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 7405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2165 0.098 - 0.196: 48 0.196 - 0.294: 0 0.294 - 0.392: 0 0.392 - 0.490: 6 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 -2.84 -0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" P DT J 69 " pdb=" OP1 DT J 69 " pdb=" OP2 DT J 69 " pdb=" O5' DT J 69 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.27e+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 -2.79 -0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 2216 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C ASP F 24 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.025 2.00e-02 2.50e+03 1.03e-02 3.15e+00 pdb=" N9 DG I 47 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 37 " 0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 38 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.022 5.00e-02 4.00e+02 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2675 2.81 - 3.33: 10636 3.33 - 3.85: 22521 3.85 - 4.38: 26626 4.38 - 4.90: 38325 Nonbonded interactions: 100783 Sorted by model distance: nonbonded pdb=" OE1 GLU K 51 " pdb=" OH TYR K 59 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.303 3.040 nonbonded pdb=" O ASP F 24 " pdb=" OD1 ASP F 24 " model vdw 2.309 3.040 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.313 3.120 nonbonded pdb=" O THR E 58 " pdb=" OG1 THR E 58 " model vdw 2.315 3.040 ... (remaining 100778 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=0.62 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: 1.360 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: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.240 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 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 0.071 13498 Z= 0.212 Angle : 0.600 11.331 19466 Z= 0.360 Chirality : 0.042 0.490 2219 Planarity : 0.004 0.038 1463 Dihedral : 27.354 179.059 5816 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.42 % Allowed : 20.34 % Favored : 79.24 % 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: 2.59 (0.30), residues: 831 helix: 3.13 (0.22), residues: 523 sheet: 1.31 (0.88), residues: 26 loop : -1.14 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 68 PHE 0.008 0.001 PHE F 61 TYR 0.008 0.001 TYR H 37 ARG 0.006 0.000 ARG D 83 *********************** 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 134 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 131 time to evaluate : 1.064 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 133 average time/residue: 0.3697 time to fit residues: 63.6308 Evaluate side-chains 129 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 127 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain F residue 85 ASP 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: 0.9980 chunk 27 optimal weight: 4.9990 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 2.9990 chunk 84 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 0.0070 chunk 63 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- 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** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.0682 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= 0.229 Angle : 0.546 5.972 19466 Z= 0.332 Chirality : 0.034 0.138 2219 Planarity : 0.004 0.038 1463 Dihedral : 29.429 179.076 4118 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.10 % Allowed : 19.50 % Favored : 78.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.69 (0.30), residues: 831 helix: 3.05 (0.22), residues: 547 sheet: 1.46 (0.89), residues: 26 loop : -1.17 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE F 61 TYR 0.007 0.001 TYR H 37 ARG 0.005 0.000 ARG D 83 *********************** 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: 15 poor density : 129 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8022 (t0) cc_final: 0.7718 (t0) REVERT: B 27 GLN cc_start: 0.9149 (OUTLIER) cc_final: 0.8545 (mp10) REVERT: H 31 LYS cc_start: 0.8639 (mmmt) cc_final: 0.8360 (mmmt) REVERT: K 1 MET cc_start: 0.7214 (ppp) cc_final: 0.6845 (ppp) outliers start: 15 outliers final: 12 residues processed: 136 average time/residue: 0.3710 time to fit residues: 65.3346 Evaluate side-chains 134 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 30 optimal weight: 0.1980 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 87 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 3.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS D 44 GLN ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 13498 Z= 0.418 Angle : 0.624 6.977 19466 Z= 0.374 Chirality : 0.039 0.151 2219 Planarity : 0.005 0.043 1463 Dihedral : 29.526 179.440 4114 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.79 % Allowed : 18.65 % Favored : 77.56 % 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 (0.30), residues: 831 helix: 2.77 (0.22), residues: 544 sheet: 1.26 (0.90), residues: 26 loop : -1.34 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 75 PHE 0.012 0.002 PHE H 67 TYR 0.009 0.001 TYR C 50 ARG 0.004 0.000 ARG D 83 *********************** 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 149 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 122 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: B 27 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8554 (mp10) REVERT: B 92 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8152 (ttp80) REVERT: F 92 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8413 (mtp85) REVERT: H 31 LYS cc_start: 0.8758 (mmmt) cc_final: 0.8298 (mmmt) REVERT: K 1 MET cc_start: 0.7489 (ppp) cc_final: 0.6966 (ppp) outliers start: 27 outliers final: 19 residues processed: 142 average time/residue: 0.3758 time to fit residues: 68.9889 Evaluate side-chains 143 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 97 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 13498 Z= 0.199 Angle : 0.561 6.565 19466 Z= 0.342 Chirality : 0.035 0.143 2219 Planarity : 0.004 0.061 1463 Dihedral : 29.515 179.297 4114 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.65 % Allowed : 19.35 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.30), residues: 831 helix: 2.86 (0.22), residues: 549 sheet: 0.76 (0.82), residues: 26 loop : -1.31 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.010 0.001 PHE F 61 TYR 0.008 0.001 TYR C 50 ARG 0.005 0.000 ARG D 83 *********************** 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 150 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 124 time to evaluate : 1.069 Fit side-chains REVERT: A 59 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.7734 (pm20) REVERT: B 27 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8522 (mp10) REVERT: B 92 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8094 (ttp80) REVERT: F 92 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8358 (mtp85) REVERT: H 31 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8246 (mmmt) REVERT: K 1 MET cc_start: 0.7447 (ppp) cc_final: 0.7086 (ppp) outliers start: 26 outliers final: 18 residues processed: 143 average time/residue: 0.3725 time to fit residues: 68.8569 Evaluate side-chains 142 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 120 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR 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: 3.9990 chunk 77 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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: 0.8835 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 13498 Z= 0.390 Angle : 0.617 6.509 19466 Z= 0.371 Chirality : 0.039 0.152 2219 Planarity : 0.005 0.043 1463 Dihedral : 29.542 179.684 4114 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.91 % Allowed : 18.93 % Favored : 76.16 % 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: 2.15 (0.30), residues: 831 helix: 2.72 (0.22), residues: 544 sheet: 0.53 (0.83), residues: 26 loop : -1.45 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.012 0.002 PHE H 67 TYR 0.009 0.001 TYR H 39 ARG 0.006 0.000 ARG D 83 *********************** 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 155 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 0.960 Fit side-chains REVERT: A 59 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: B 27 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8545 (mp10) REVERT: B 92 ARG cc_start: 0.9185 (OUTLIER) cc_final: 0.8150 (ttp80) REVERT: F 92 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.8389 (mtp85) REVERT: G 42 ARG cc_start: 0.8950 (OUTLIER) cc_final: 0.8100 (mtm180) REVERT: H 31 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8483 (mmmt) REVERT: K 1 MET cc_start: 0.7687 (ppp) cc_final: 0.6929 (ppp) outliers start: 35 outliers final: 27 residues processed: 146 average time/residue: 0.3926 time to fit residues: 72.7489 Evaluate side-chains 148 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 116 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 35 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 61 optimal weight: 0.3980 chunk 25 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 48 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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: 0.8769 moved from start: 0.1217 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= 0.187 Angle : 0.551 5.848 19466 Z= 0.333 Chirality : 0.034 0.144 2219 Planarity : 0.004 0.042 1463 Dihedral : 29.425 178.795 4114 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.65 % Allowed : 20.76 % Favored : 75.60 % 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: 2.59 (0.30), residues: 831 helix: 3.11 (0.22), residues: 544 sheet: 0.53 (0.85), residues: 26 loop : -1.38 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE F 61 TYR 0.007 0.001 TYR H 37 ARG 0.005 0.000 ARG D 83 *********************** 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 155 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.951 Fit side-chains REVERT: A 59 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7645 (pm20) REVERT: B 27 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8546 (mp10) REVERT: B 92 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8129 (ttp80) REVERT: D 30 ARG cc_start: 0.8279 (mtp85) cc_final: 0.8021 (mtt180) REVERT: E 115 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8330 (ttmm) REVERT: F 92 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8359 (mtp85) REVERT: G 42 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8011 (mtm180) REVERT: H 31 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8254 (mmtm) REVERT: H 65 ASP cc_start: 0.9275 (t0) cc_final: 0.8966 (t0) REVERT: K 1 MET cc_start: 0.7890 (ppp) cc_final: 0.7000 (ppp) outliers start: 26 outliers final: 14 residues processed: 145 average time/residue: 0.3782 time to fit residues: 70.6668 Evaluate side-chains 144 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 124 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 70 VAL 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: 1.9990 chunk 59 optimal weight: 2.9990 chunk 76 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 104 optimal weight: 0.0670 chunk 65 optimal weight: 0.9980 chunk 63 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 overall best weight: 0.7922 ------------------------------------------------------------------------------- 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: 0.8703 moved from start: 0.1422 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= 0.168 Angle : 0.520 7.161 19466 Z= 0.315 Chirality : 0.033 0.161 2219 Planarity : 0.004 0.041 1463 Dihedral : 29.359 178.768 4114 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.81 % Allowed : 21.60 % Favored : 75.60 % 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: 2.91 (0.30), residues: 831 helix: 3.30 (0.22), residues: 553 sheet: 0.61 (0.85), residues: 26 loop : -1.26 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 75 PHE 0.008 0.001 PHE F 61 TYR 0.008 0.001 TYR K 59 ARG 0.007 0.000 ARG D 83 *********************** 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 157 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.041 Fit side-chains REVERT: B 27 GLN cc_start: 0.9085 (OUTLIER) cc_final: 0.8581 (mp10) REVERT: B 92 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8126 (ttp80) REVERT: D 30 ARG cc_start: 0.8287 (mtp85) cc_final: 0.7938 (mtt180) REVERT: F 92 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.8356 (mtp85) REVERT: G 42 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8000 (mtm180) REVERT: H 65 ASP cc_start: 0.9237 (t0) cc_final: 0.8864 (t0) REVERT: K 1 MET cc_start: 0.7940 (ppp) cc_final: 0.7239 (ppp) outliers start: 20 outliers final: 8 residues processed: 152 average time/residue: 0.3503 time to fit residues: 69.4870 Evaluate side-chains 141 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 129 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 0.0870 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 9 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 94 optimal weight: 6.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.1564 ------------------------------------------------------------------------------- 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: 0.8728 moved from start: 0.1442 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= 0.192 Angle : 0.526 5.188 19466 Z= 0.319 Chirality : 0.033 0.159 2219 Planarity : 0.004 0.040 1463 Dihedral : 29.350 178.216 4114 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.10 % Allowed : 22.86 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.30), residues: 831 helix: 3.30 (0.22), residues: 554 sheet: 0.75 (0.97), residues: 20 loop : -1.24 (0.36), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.008 0.001 TYR H 37 ARG 0.006 0.000 ARG D 83 *********************** 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 151 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.012 Fit side-chains REVERT: B 24 ASP cc_start: 0.8092 (t0) cc_final: 0.7872 (t0) REVERT: B 27 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8571 (mp10) REVERT: B 92 ARG cc_start: 0.9077 (OUTLIER) cc_final: 0.8152 (ttp80) REVERT: D 30 ARG cc_start: 0.8282 (mtp85) cc_final: 0.8021 (mtt180) REVERT: F 92 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8370 (mtp85) REVERT: G 42 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.7989 (mtm180) REVERT: H 65 ASP cc_start: 0.9246 (t0) cc_final: 0.8851 (t0) REVERT: K 1 MET cc_start: 0.8018 (ppp) cc_final: 0.7266 (ppp) outliers start: 15 outliers final: 10 residues processed: 147 average time/residue: 0.3625 time to fit residues: 69.0680 Evaluate side-chains 144 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 130 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain K residue 72 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN E 55 GLN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 13498 Z= 0.326 Angle : 0.595 7.287 19466 Z= 0.355 Chirality : 0.037 0.166 2219 Planarity : 0.004 0.040 1463 Dihedral : 29.426 179.138 4114 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.52 % Allowed : 23.28 % Favored : 74.19 % 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: 2.53 (0.30), residues: 831 helix: 3.00 (0.22), residues: 552 sheet: 0.77 (1.10), residues: 20 loop : -1.39 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.013 0.002 PHE H 67 TYR 0.008 0.001 TYR K 59 ARG 0.006 0.000 ARG D 83 *********************** 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 139 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 121 time to evaluate : 1.047 Fit side-chains REVERT: A 59 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7751 (pm20) REVERT: B 27 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8548 (mp10) REVERT: B 92 ARG cc_start: 0.9172 (OUTLIER) cc_final: 0.8156 (ttp80) REVERT: D 30 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8042 (mtt180) REVERT: D 32 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8270 (mt-10) REVERT: F 92 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8386 (mtp85) REVERT: G 42 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8082 (mtm180) REVERT: H 31 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8351 (mmtm) REVERT: K 1 MET cc_start: 0.8056 (ppp) cc_final: 0.7260 (ppp) outliers start: 18 outliers final: 11 residues processed: 135 average time/residue: 0.3683 time to fit residues: 63.8534 Evaluate side-chains 136 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 105 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 102 optimal weight: 8.9990 chunk 62 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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: 0.8774 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13498 Z= 0.184 Angle : 0.564 7.032 19466 Z= 0.338 Chirality : 0.035 0.244 2219 Planarity : 0.004 0.041 1463 Dihedral : 29.407 178.755 4114 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.10 % Allowed : 23.56 % Favored : 74.33 % 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: 2.61 (0.30), residues: 831 helix: 3.10 (0.22), residues: 549 sheet: 0.51 (1.04), residues: 20 loop : -1.38 (0.36), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.009 0.001 TYR H 37 ARG 0.007 0.000 ARG D 83 ********************** 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 140 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 125 time to evaluate : 1.049 Fit side-chains REVERT: A 59 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7643 (pm20) REVERT: B 27 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8512 (mp10) REVERT: B 92 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8115 (ttp80) REVERT: D 30 ARG cc_start: 0.8323 (mtp85) cc_final: 0.8063 (mtt180) REVERT: F 92 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8367 (mtp85) REVERT: G 42 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8047 (mtm180) REVERT: H 31 LYS cc_start: 0.8853 (mmmt) cc_final: 0.8383 (mmtm) REVERT: H 65 ASP cc_start: 0.9267 (t0) cc_final: 0.8918 (t0) REVERT: K 3 ILE cc_start: 0.7728 (mm) cc_final: 0.7468 (mm) outliers start: 15 outliers final: 10 residues processed: 137 average time/residue: 0.3709 time to fit residues: 65.3981 Evaluate side-chains 138 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG 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: 5.9990 chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.090858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.060817 restraints weight = 28449.888| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 1.87 r_work: 0.2627 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2630 r_free = 0.2630 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.1430 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= 0.246 Angle : 0.566 6.316 19466 Z= 0.338 Chirality : 0.035 0.166 2219 Planarity : 0.004 0.041 1463 Dihedral : 29.379 178.518 4114 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.10 % Allowed : 23.14 % Favored : 74.75 % 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: 2.61 (0.30), residues: 831 helix: 3.11 (0.22), residues: 552 sheet: 0.71 (1.06), residues: 20 loop : -1.44 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE F 61 TYR 0.009 0.001 TYR H 37 ARG 0.007 0.000 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2245.37 seconds wall clock time: 40 minutes 43.17 seconds (2443.17 seconds total)