Starting phenix.real_space_refine on Sun Oct 13 16:11:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg2_43198/10_2024/8vg2_43198.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg2_43198/10_2024/8vg2_43198.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg2_43198/10_2024/8vg2_43198.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg2_43198/10_2024/8vg2_43198.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg2_43198/10_2024/8vg2_43198.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vg2_43198/10_2024/8vg2_43198.cif" } resolution = 3.04 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 392 5.49 5 S 21 5.16 5 C 8651 2.51 5 N 2930 2.21 5 O 3695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 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: 15689 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 858 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" 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: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "F" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 936 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "H" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 774 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "I" Number of atoms: 3998 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3998 Classifications: {'DNA': 196} Link IDs: {'rna3p': 195} Chain: "J" Number of atoms: 4038 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 4038 Classifications: {'DNA': 196} Link IDs: {'rna3p': 195} Chain: "O" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 856 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "U" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 8.93, per 1000 atoms: 0.57 Number of scatterers: 15689 At special positions: 0 Unit cell: (86.592, 121.44, 195.36, 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 21 16.00 P 392 15.00 O 3695 8.00 N 2930 7.00 C 8651 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: 3.79 Conformation dependent library (CDL) restraints added in 1.2 seconds 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1800 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 12 sheets defined 68.0% alpha, 3.7% beta 187 base pairs and 339 stacking pairs defined. Time for finding SS restraints: 7.07 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.957A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.564A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.632A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.522A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.408A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 125 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.895A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.682A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 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 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 125 Processing helix chain 'O' and resid 174 through 186 removed outlier: 3.825A pdb=" N ALA O 186 " --> pdb=" O ALA O 182 " (cutoff:3.500A) Processing helix chain 'O' and resid 192 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.801A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 Processing helix chain 'O' and resid 248 through 251 Processing helix chain 'U' and resid 38 through 51 removed outlier: 3.606A pdb=" N LEU U 42 " --> pdb=" O PRO U 38 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER U 50 " --> pdb=" O ALA U 46 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS U 51 " --> pdb=" O VAL U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 58 through 69 Processing helix chain 'U' and resid 71 through 74 Processing helix chain 'U' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.012A 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 96 through 98 removed outlier: 6.578A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.259A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.838A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.940A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'O' and resid 228 through 231 removed outlier: 3.538A pdb=" N TYR O 243 " --> pdb=" O VAL O 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'U' and resid 56 through 57 486 hydrogen bonds defined for protein. 1422 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 471 hydrogen bonds 942 hydrogen bond angles 0 basepair planarities 187 basepair parallelities 339 stacking parallelities Total time for adding SS restraints: 6.87 Time building geometry restraints manager: 4.40 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: 3115 1.33 - 1.45: 5281 1.45 - 1.57: 7566 1.57 - 1.69: 782 1.69 - 1.81: 35 Bond restraints: 16779 Sorted by residual: bond pdb=" N LYS H 28 " pdb=" CA LYS H 28 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.90e-02 2.77e+03 3.18e+00 bond pdb=" N LYS B 20 " pdb=" CA LYS B 20 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N LYS A 36 " pdb=" CA LYS A 36 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.09e+00 bond pdb=" N LYS G 9 " pdb=" CA LYS G 9 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.98e+00 bond pdb=" N LYS D 30 " pdb=" CA LYS D 30 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 16774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 22684 1.16 - 2.31: 1300 2.31 - 3.47: 303 3.47 - 4.63: 29 4.63 - 5.78: 9 Bond angle restraints: 24325 Sorted by residual: angle pdb=" CA TRP O 214 " pdb=" CB TRP O 214 " pdb=" CG TRP O 214 " ideal model delta sigma weight residual 113.60 119.13 -5.53 1.90e+00 2.77e-01 8.48e+00 angle pdb=" C2' DT I 88 " pdb=" C1' DT I 88 " pdb=" N1 DT I 88 " ideal model delta sigma weight residual 113.50 117.71 -4.21 1.50e+00 4.44e-01 7.88e+00 angle pdb=" C2' DT J 131 " pdb=" C1' DT J 131 " pdb=" N1 DT J 131 " ideal model delta sigma weight residual 113.50 117.59 -4.09 1.50e+00 4.44e-01 7.42e+00 angle pdb=" C2' DC I 151 " pdb=" C1' DC I 151 " pdb=" N1 DC I 151 " ideal model delta sigma weight residual 113.50 117.30 -3.80 1.50e+00 4.44e-01 6.42e+00 angle pdb=" C2' DC J 50 " pdb=" C1' DC J 50 " pdb=" N1 DC J 50 " ideal model delta sigma weight residual 113.50 117.09 -3.59 1.50e+00 4.44e-01 5.74e+00 ... (remaining 24320 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.10: 6209 17.10 - 34.21: 1286 34.21 - 51.31: 1119 51.31 - 68.41: 490 68.41 - 85.51: 21 Dihedral angle restraints: 9125 sinusoidal: 6332 harmonic: 2793 Sorted by residual: dihedral pdb=" CA PHE E 84 " pdb=" C PHE E 84 " pdb=" N GLN E 85 " pdb=" CA GLN E 85 " ideal model delta harmonic sigma weight residual 180.00 164.39 15.61 0 5.00e+00 4.00e-02 9.75e+00 dihedral pdb=" CA ARG E 128 " pdb=" CB ARG E 128 " pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -120.60 -59.40 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" N LYS D 30 " pdb=" CA LYS D 30 " pdb=" CB LYS D 30 " pdb=" CG LYS D 30 " ideal model delta sinusoidal sigma weight residual -60.00 -117.86 57.86 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 9122 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1764 0.029 - 0.058: 581 0.058 - 0.087: 330 0.087 - 0.116: 61 0.116 - 0.146: 8 Chirality restraints: 2744 Sorted by residual: chirality pdb=" CA ILE B 29 " pdb=" N ILE B 29 " pdb=" C ILE B 29 " pdb=" CB ILE B 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.30e-01 chirality pdb=" CA ILE C 111 " pdb=" N ILE C 111 " pdb=" C ILE C 111 " pdb=" CB ILE C 111 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 2741 not shown) Planarity restraints: 1712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 88 " 0.024 2.00e-02 2.50e+03 1.20e-02 3.62e+00 pdb=" N1 DT I 88 " -0.027 2.00e-02 2.50e+03 pdb=" C2 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 88 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 88 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 88 " 0.005 2.00e-02 2.50e+03 pdb=" O4 DT I 88 " 0.009 2.00e-02 2.50e+03 pdb=" C5 DT I 88 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 88 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DT I 88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 86 " 0.023 2.00e-02 2.50e+03 1.17e-02 3.41e+00 pdb=" N1 DT I 86 " -0.027 2.00e-02 2.50e+03 pdb=" C2 DT I 86 " -0.003 2.00e-02 2.50e+03 pdb=" O2 DT I 86 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 86 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DT I 86 " 0.003 2.00e-02 2.50e+03 pdb=" O4 DT I 86 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 86 " 0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 86 " -0.003 2.00e-02 2.50e+03 pdb=" C6 DT I 86 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO O 238 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " 0.025 5.00e-02 4.00e+02 ... (remaining 1709 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1841 2.76 - 3.29: 13546 3.29 - 3.83: 30647 3.83 - 4.36: 36360 4.36 - 4.90: 51294 Nonbonded interactions: 133688 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.219 3.040 nonbonded pdb=" NZ LYS B 91 " pdb=" OE2 GLU H 71 " model vdw 2.235 3.120 nonbonded pdb=" OD2 ASP B 68 " pdb=" NE2 GLN B 93 " model vdw 2.313 3.120 nonbonded pdb=" OG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 2.326 3.040 nonbonded pdb=" N GLU E 59 " pdb=" OE1 GLU E 59 " model vdw 2.340 3.120 ... (remaining 133683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 9 through 119) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 125) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 39.930 Find NCS groups from input model: 0.300 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: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 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 0.041 16779 Z= 0.238 Angle : 0.632 5.783 24325 Z= 0.397 Chirality : 0.037 0.146 2744 Planarity : 0.004 0.045 1712 Dihedral : 25.723 85.514 7325 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.11 % Allowed : 1.69 % Favored : 98.20 % Rotamer: Outliers : 0.25 % Allowed : 1.86 % Favored : 97.89 % 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: 2.46 (0.27), residues: 945 helix: 2.67 (0.21), residues: 616 sheet: -0.74 (1.27), residues: 20 loop : -0.40 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP O 214 HIS 0.003 0.001 HIS O 220 PHE 0.007 0.001 PHE A 67 TYR 0.008 0.001 TYR B 51 ARG 0.004 0.000 ARG O 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 190 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8675 (tt0) cc_final: 0.8297 (tt0) REVERT: A 123 ASP cc_start: 0.9411 (m-30) cc_final: 0.9151 (m-30) REVERT: D 68 ASP cc_start: 0.9004 (t0) cc_final: 0.8538 (t0) REVERT: D 72 ARG cc_start: 0.9138 (mtt180) cc_final: 0.8812 (mtt180) REVERT: F 59 LYS cc_start: 0.9227 (tttp) cc_final: 0.9014 (tttp) REVERT: G 101 THR cc_start: 0.9178 (t) cc_final: 0.8934 (t) REVERT: H 68 ASP cc_start: 0.9269 (t0) cc_final: 0.8868 (t0) REVERT: H 101 LEU cc_start: 0.9300 (mm) cc_final: 0.9006 (mm) REVERT: H 113 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8593 (mm-30) REVERT: O 201 MET cc_start: 0.6965 (ttt) cc_final: 0.6383 (tmm) REVERT: O 214 TRP cc_start: 0.7558 (p-90) cc_final: 0.7253 (p-90) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.4761 time to fit residues: 119.0372 Evaluate side-chains 167 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 118 optimal weight: 30.0000 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN B 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16779 Z= 0.324 Angle : 0.572 6.656 24325 Z= 0.344 Chirality : 0.036 0.131 2744 Planarity : 0.004 0.053 1712 Dihedral : 29.831 81.001 5388 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 1.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.57 % Rotamer: Outliers : 0.87 % Allowed : 4.46 % Favored : 94.67 % 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: 2.54 (0.27), residues: 945 helix: 2.71 (0.21), residues: 625 sheet: -0.72 (1.21), residues: 20 loop : -0.41 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 214 HIS 0.003 0.001 HIS D 49 PHE 0.010 0.001 PHE A 67 TYR 0.009 0.001 TYR B 51 ARG 0.005 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 167 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9437 (m-30) cc_final: 0.9191 (m-30) REVERT: B 93 GLN cc_start: 0.8868 (mm-40) cc_final: 0.8627 (mm110) REVERT: C 99 ARG cc_start: 0.8426 (mmm160) cc_final: 0.8168 (mtp85) REVERT: D 68 ASP cc_start: 0.9054 (t0) cc_final: 0.8803 (t0) REVERT: E 73 GLU cc_start: 0.8834 (tt0) cc_final: 0.8521 (tt0) REVERT: F 35 ARG cc_start: 0.8829 (ttm-80) cc_final: 0.8515 (ttp80) REVERT: G 92 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8733 (mm-30) REVERT: H 68 ASP cc_start: 0.9191 (t0) cc_final: 0.8816 (t0) REVERT: H 101 LEU cc_start: 0.9324 (mm) cc_final: 0.8954 (mm) REVERT: H 113 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8486 (mm-30) REVERT: O 201 MET cc_start: 0.6938 (ttt) cc_final: 0.6451 (tmm) REVERT: O 214 TRP cc_start: 0.7407 (p-90) cc_final: 0.6994 (p-90) outliers start: 7 outliers final: 5 residues processed: 170 average time/residue: 0.4437 time to fit residues: 101.1221 Evaluate side-chains 166 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 161 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 117 optimal weight: 6.9990 chunk 40 optimal weight: 0.5980 chunk 94 optimal weight: 20.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16779 Z= 0.312 Angle : 0.558 6.160 24325 Z= 0.336 Chirality : 0.035 0.129 2744 Planarity : 0.004 0.056 1712 Dihedral : 29.961 80.493 5388 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.67 % Rotamer: Outliers : 1.12 % Allowed : 6.20 % Favored : 92.69 % 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: 2.57 (0.27), residues: 945 helix: 2.72 (0.20), residues: 625 sheet: -0.54 (1.22), residues: 20 loop : -0.38 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 214 HIS 0.003 0.001 HIS D 49 PHE 0.010 0.001 PHE A 67 TYR 0.010 0.001 TYR D 37 ARG 0.005 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 169 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9428 (m-30) cc_final: 0.9203 (m-30) REVERT: B 93 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8605 (mm110) REVERT: E 73 GLU cc_start: 0.8850 (tt0) cc_final: 0.8546 (tt0) REVERT: F 35 ARG cc_start: 0.8786 (ttm-80) cc_final: 0.8469 (ttp80) REVERT: G 92 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8706 (mm-30) REVERT: H 68 ASP cc_start: 0.9231 (t0) cc_final: 0.8821 (t0) REVERT: H 101 LEU cc_start: 0.9332 (mm) cc_final: 0.8894 (mm) REVERT: H 113 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8496 (mm-30) REVERT: O 201 MET cc_start: 0.7002 (ttt) cc_final: 0.6482 (tmm) REVERT: O 214 TRP cc_start: 0.7395 (p-90) cc_final: 0.7023 (p-90) outliers start: 9 outliers final: 8 residues processed: 173 average time/residue: 0.4643 time to fit residues: 106.6629 Evaluate side-chains 175 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain O residue 261 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 8.9990 chunk 88 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 79 optimal weight: 6.9990 chunk 118 optimal weight: 8.9990 chunk 125 optimal weight: 9.9990 chunk 62 optimal weight: 0.9990 chunk 112 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN H 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16779 Z= 0.205 Angle : 0.543 9.503 24325 Z= 0.329 Chirality : 0.033 0.131 2744 Planarity : 0.004 0.057 1712 Dihedral : 29.970 80.807 5388 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.78 % Rotamer: Outliers : 1.12 % Allowed : 7.81 % Favored : 91.08 % 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: 2.63 (0.27), residues: 945 helix: 2.76 (0.20), residues: 625 sheet: -0.48 (1.21), residues: 20 loop : -0.34 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.006 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9410 (m-30) cc_final: 0.9171 (m-30) REVERT: B 93 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8563 (mm110) REVERT: E 59 GLU cc_start: 0.9023 (pm20) cc_final: 0.8569 (pm20) REVERT: E 131 ARG cc_start: 0.9373 (OUTLIER) cc_final: 0.8648 (mtp180) REVERT: F 35 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8441 (ttp80) REVERT: G 101 THR cc_start: 0.9274 (OUTLIER) cc_final: 0.9024 (t) REVERT: H 68 ASP cc_start: 0.9199 (t0) cc_final: 0.8785 (t0) REVERT: H 101 LEU cc_start: 0.9338 (mm) cc_final: 0.8917 (mm) REVERT: H 113 GLU cc_start: 0.8818 (mm-30) cc_final: 0.8465 (mm-30) REVERT: O 201 MET cc_start: 0.6998 (ttt) cc_final: 0.6482 (tmm) REVERT: O 214 TRP cc_start: 0.7398 (p-90) cc_final: 0.7001 (p-90) outliers start: 9 outliers final: 6 residues processed: 171 average time/residue: 0.4857 time to fit residues: 110.1540 Evaluate side-chains 173 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain O residue 261 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 93 optimal weight: 20.0000 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 16779 Z= 0.444 Angle : 0.606 6.122 24325 Z= 0.360 Chirality : 0.040 0.132 2744 Planarity : 0.004 0.059 1712 Dihedral : 30.314 81.037 5388 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 1.49 % Allowed : 8.18 % Favored : 90.33 % 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: 2.41 (0.27), residues: 945 helix: 2.59 (0.20), residues: 625 sheet: -0.56 (1.21), residues: 20 loop : -0.43 (0.35), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 214 HIS 0.003 0.001 HIS D 49 PHE 0.010 0.001 PHE A 67 TYR 0.010 0.002 TYR H 121 ARG 0.009 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9437 (m-30) cc_final: 0.9231 (m-30) REVERT: E 73 GLU cc_start: 0.8874 (OUTLIER) cc_final: 0.8590 (tt0) REVERT: E 131 ARG cc_start: 0.9421 (OUTLIER) cc_final: 0.8894 (mtp180) REVERT: F 35 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8439 (ttp80) REVERT: G 92 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8717 (mm-30) REVERT: H 68 ASP cc_start: 0.9280 (t0) cc_final: 0.8885 (t0) REVERT: H 101 LEU cc_start: 0.9384 (mm) cc_final: 0.8858 (mm) REVERT: H 113 GLU cc_start: 0.8882 (mm-30) cc_final: 0.8519 (mm-30) REVERT: O 201 MET cc_start: 0.6948 (ttt) cc_final: 0.6416 (tmm) REVERT: O 214 TRP cc_start: 0.7414 (p-90) cc_final: 0.7022 (p-90) outliers start: 12 outliers final: 8 residues processed: 176 average time/residue: 0.4570 time to fit residues: 106.3945 Evaluate side-chains 180 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 71 GLU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 9.9990 chunk 24 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 125 optimal weight: 9.9990 chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 66 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16779 Z= 0.186 Angle : 0.559 8.724 24325 Z= 0.336 Chirality : 0.034 0.146 2744 Planarity : 0.004 0.059 1712 Dihedral : 30.242 82.024 5388 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.78 % Rotamer: Outliers : 1.12 % Allowed : 8.80 % Favored : 90.09 % 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: 2.57 (0.27), residues: 945 helix: 2.72 (0.20), residues: 625 sheet: -0.61 (1.20), residues: 20 loop : -0.38 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 214 HIS 0.002 0.001 HIS F 75 PHE 0.008 0.001 PHE A 67 TYR 0.012 0.001 TYR B 51 ARG 0.009 0.000 ARG O 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 167 time to evaluate : 1.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9419 (m-30) cc_final: 0.9186 (m-30) REVERT: C 13 LYS cc_start: 0.8937 (mmmt) cc_final: 0.8388 (tptt) REVERT: E 131 ARG cc_start: 0.9386 (OUTLIER) cc_final: 0.8753 (mtp180) REVERT: F 35 ARG cc_start: 0.8764 (ttm-80) cc_final: 0.8451 (ttp80) REVERT: G 101 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9105 (t) REVERT: H 68 ASP cc_start: 0.9211 (t0) cc_final: 0.8801 (t0) REVERT: H 101 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8827 (mm) REVERT: H 113 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8435 (mm-30) REVERT: O 201 MET cc_start: 0.6948 (ttt) cc_final: 0.6423 (tmm) REVERT: O 214 TRP cc_start: 0.7417 (p-90) cc_final: 0.7009 (p-90) outliers start: 9 outliers final: 5 residues processed: 171 average time/residue: 0.4431 time to fit residues: 100.8929 Evaluate side-chains 173 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 165 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 105 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 57 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16779 Z= 0.336 Angle : 0.574 9.463 24325 Z= 0.343 Chirality : 0.036 0.131 2744 Planarity : 0.004 0.059 1712 Dihedral : 30.191 80.296 5388 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 1.12 % Allowed : 8.92 % Favored : 89.96 % 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: 2.52 (0.27), residues: 945 helix: 2.70 (0.20), residues: 625 sheet: -0.49 (1.20), residues: 20 loop : -0.44 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.010 0.001 TYR G 57 ARG 0.008 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 171 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9427 (m-30) cc_final: 0.9214 (m-30) REVERT: C 13 LYS cc_start: 0.8870 (mmmt) cc_final: 0.8373 (tptt) REVERT: E 73 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8613 (tt0) REVERT: E 131 ARG cc_start: 0.9419 (OUTLIER) cc_final: 0.8814 (mtp180) REVERT: F 35 ARG cc_start: 0.8789 (ttm-80) cc_final: 0.8461 (ttp80) REVERT: G 101 THR cc_start: 0.9355 (OUTLIER) cc_final: 0.9136 (t) REVERT: H 68 ASP cc_start: 0.9246 (t0) cc_final: 0.8857 (t0) REVERT: H 101 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8833 (mm) REVERT: H 113 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8476 (mm-30) REVERT: O 201 MET cc_start: 0.6948 (ttt) cc_final: 0.6412 (tmm) REVERT: O 214 TRP cc_start: 0.7360 (p-90) cc_final: 0.6914 (p-90) outliers start: 9 outliers final: 4 residues processed: 175 average time/residue: 0.4805 time to fit residues: 111.4338 Evaluate side-chains 176 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 168 time to evaluate : 1.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 37 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 113 optimal weight: 8.9990 chunk 120 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16779 Z= 0.202 Angle : 0.560 11.876 24325 Z= 0.336 Chirality : 0.033 0.132 2744 Planarity : 0.004 0.059 1712 Dihedral : 30.187 80.882 5388 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 1.36 % Allowed : 9.17 % Favored : 89.47 % 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: 2.60 (0.27), residues: 945 helix: 2.76 (0.20), residues: 625 sheet: -0.51 (1.20), residues: 20 loop : -0.41 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 214 HIS 0.002 0.001 HIS F 75 PHE 0.009 0.001 PHE A 67 TYR 0.013 0.001 TYR H 37 ARG 0.010 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 167 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9406 (m-30) cc_final: 0.9176 (m-30) REVERT: A 131 ARG cc_start: 0.9375 (OUTLIER) cc_final: 0.9107 (mtt180) REVERT: C 13 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8418 (tptt) REVERT: E 131 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.8755 (mtp180) REVERT: F 35 ARG cc_start: 0.8774 (ttm-80) cc_final: 0.8458 (ttp80) REVERT: G 101 THR cc_start: 0.9339 (OUTLIER) cc_final: 0.9114 (t) REVERT: H 68 ASP cc_start: 0.9224 (t0) cc_final: 0.8822 (t0) REVERT: H 101 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.8933 (mm) REVERT: H 113 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8424 (mm-30) REVERT: O 201 MET cc_start: 0.7007 (ttt) cc_final: 0.6478 (tmm) REVERT: O 214 TRP cc_start: 0.7367 (p-90) cc_final: 0.6930 (p-90) REVERT: U 108 LYS cc_start: 0.8371 (mppt) cc_final: 0.8159 (tppt) outliers start: 11 outliers final: 7 residues processed: 172 average time/residue: 0.4710 time to fit residues: 107.2865 Evaluate side-chains 176 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 165 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 76 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 16779 Z= 0.347 Angle : 0.586 10.147 24325 Z= 0.348 Chirality : 0.036 0.132 2744 Planarity : 0.004 0.059 1712 Dihedral : 30.209 80.381 5388 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 1.24 % Allowed : 9.67 % Favored : 89.10 % 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: 2.51 (0.27), residues: 945 helix: 2.69 (0.20), residues: 625 sheet: -0.48 (1.20), residues: 20 loop : -0.46 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 214 HIS 0.003 0.001 HIS D 49 PHE 0.009 0.001 PHE A 67 TYR 0.010 0.001 TYR G 57 ARG 0.010 0.000 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9419 (m-30) cc_final: 0.9208 (m-30) REVERT: A 131 ARG cc_start: 0.9383 (OUTLIER) cc_final: 0.9121 (mtt180) REVERT: E 73 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8614 (tt0) REVERT: E 131 ARG cc_start: 0.9416 (OUTLIER) cc_final: 0.8816 (mtp180) REVERT: F 35 ARG cc_start: 0.8796 (ttm-80) cc_final: 0.8456 (ttp80) REVERT: H 68 ASP cc_start: 0.9259 (t0) cc_final: 0.8831 (t0) REVERT: H 101 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.8837 (mm) REVERT: H 113 GLU cc_start: 0.8804 (mm-30) cc_final: 0.8454 (mm-30) REVERT: O 201 MET cc_start: 0.6942 (ttt) cc_final: 0.6395 (tmm) REVERT: O 214 TRP cc_start: 0.7328 (p-90) cc_final: 0.6884 (p-90) outliers start: 10 outliers final: 6 residues processed: 173 average time/residue: 0.4845 time to fit residues: 110.8427 Evaluate side-chains 177 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 1.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 129 optimal weight: 20.0000 chunk 119 optimal weight: 0.0870 chunk 103 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16779 Z= 0.246 Angle : 0.575 11.019 24325 Z= 0.342 Chirality : 0.034 0.135 2744 Planarity : 0.004 0.059 1712 Dihedral : 30.230 80.654 5388 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 1.24 % Allowed : 9.67 % Favored : 89.10 % 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: 2.58 (0.27), residues: 945 helix: 2.75 (0.20), residues: 625 sheet: -0.43 (1.21), residues: 20 loop : -0.43 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.016 0.001 TYR H 37 ARG 0.009 0.000 ARG D 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1890 Ramachandran restraints generated. 945 Oldfield, 0 Emsley, 945 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 168 time to evaluate : 1.136 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.9417 (m-30) cc_final: 0.9198 (m-30) REVERT: A 131 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.9112 (mtt180) REVERT: C 13 LYS cc_start: 0.8888 (mmmt) cc_final: 0.8355 (tptt) REVERT: E 131 ARG cc_start: 0.9400 (OUTLIER) cc_final: 0.8774 (mtp180) REVERT: F 35 ARG cc_start: 0.8786 (ttm-80) cc_final: 0.8453 (ttp80) REVERT: G 101 THR cc_start: 0.9351 (OUTLIER) cc_final: 0.9132 (t) REVERT: H 68 ASP cc_start: 0.9261 (t0) cc_final: 0.8843 (t0) REVERT: H 101 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.8821 (mm) REVERT: H 113 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8421 (mm-30) REVERT: O 201 MET cc_start: 0.6940 (ttt) cc_final: 0.6397 (tmm) REVERT: O 214 TRP cc_start: 0.7328 (p-90) cc_final: 0.6878 (p-90) outliers start: 10 outliers final: 6 residues processed: 173 average time/residue: 0.4653 time to fit residues: 106.7554 Evaluate side-chains 177 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 167 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 71 GLU Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain U residue 93 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.135288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.081162 restraints weight = 27156.811| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.39 r_work: 0.2849 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8834 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16779 Z= 0.206 Angle : 0.573 15.269 24325 Z= 0.339 Chirality : 0.033 0.137 2744 Planarity : 0.004 0.059 1712 Dihedral : 30.201 80.875 5388 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.43 % Favored : 97.46 % Rotamer: Outliers : 1.24 % Allowed : 9.67 % Favored : 89.10 % 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: 2.65 (0.27), residues: 945 helix: 2.79 (0.20), residues: 625 sheet: -0.34 (1.21), residues: 20 loop : -0.41 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP O 214 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.011 0.001 TYR B 51 ARG 0.009 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3157.31 seconds wall clock time: 62 minutes 48.44 seconds (3768.44 seconds total)