Starting phenix.real_space_refine on Fri Sep 27 01:48:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfz_43195/09_2024/8vfz_43195.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfz_43195/09_2024/8vfz_43195.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfz_43195/09_2024/8vfz_43195.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfz_43195/09_2024/8vfz_43195.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfz_43195/09_2024/8vfz_43195.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vfz_43195/09_2024/8vfz_43195.cif" } resolution = 4.1 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= -0.001 sd= 0.030 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 342 5.49 5 S 28 5.16 5 C 8336 2.51 5 N 2764 2.21 5 O 3436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 14906 Number of models: 1 Model: "" Number of chains: 12 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: "I" Number of atoms: 3501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3501 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "J" Number of atoms: 3510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3510 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "P" 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: "G" Number of atoms: 931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 931 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "A" 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: "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: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 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: 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: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Time building chain proxies: 8.35, per 1000 atoms: 0.56 Number of scatterers: 14906 At special positions: 0 Unit cell: (81.84, 137.28, 199.32, 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 28 16.00 P 342 15.00 O 3436 8.00 N 2764 7.00 C 8336 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: 3.38 Conformation dependent library (CDL) restraints added in 1.1 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 66.8% alpha, 2.8% beta 171 base pairs and 289 stacking pairs defined. Time for finding SS restraints: 6.57 Creating SS restraints... Processing helix chain 'O' and resid 174 through 186 Processing helix chain 'O' and resid 192 through 204 Processing helix chain 'O' and resid 205 through 209 removed outlier: 3.522A pdb=" N GLN O 209 " --> pdb=" O TYR O 206 " (cutoff:3.500A) Processing helix chain 'O' and resid 210 through 225 removed outlier: 3.744A pdb=" N TRP O 214 " --> pdb=" O ASN O 210 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 251 removed outlier: 3.625A pdb=" N GLY O 251 " --> pdb=" O PRO O 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 248 through 251' Processing helix chain 'P' and resid 174 through 186 Processing helix chain 'P' and resid 192 through 204 Processing helix chain 'P' and resid 205 through 209 removed outlier: 3.826A pdb=" N GLN P 209 " --> pdb=" O TYR P 206 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 225 removed outlier: 3.822A pdb=" N ASN P 216 " --> pdb=" O GLN P 212 " (cutoff:3.500A) Processing helix chain 'P' and resid 248 through 251 removed outlier: 3.848A pdb=" N GLY P 251 " --> pdb=" O PRO P 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 248 through 251' Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.135A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.515A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.098A 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 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.517A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 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: 4.112A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 85 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.799A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 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: 3.579A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 85 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.638A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA H 124 " --> pdb=" O LYS H 120 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'O' and resid 228 through 231 Processing sheet with id=AA2, first strand: chain 'P' and resid 228 through 231 Processing sheet with id=AA3, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.428A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.892A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.373A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.175A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 118 through 119 478 hydrogen bonds defined for protein. 1401 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 417 hydrogen bonds 834 hydrogen bond angles 0 basepair planarities 171 basepair parallelities 289 stacking parallelities Total time for adding SS restraints: 5.83 Time building geometry restraints manager: 3.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2587 1.33 - 1.45: 5293 1.45 - 1.57: 7287 1.57 - 1.69: 682 1.69 - 1.81: 46 Bond restraints: 15895 Sorted by residual: bond pdb=" N GLY G 8 " pdb=" CA GLY G 8 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 5.92e+00 bond pdb=" CA LYS O 264 " pdb=" C LYS O 264 " ideal model delta sigma weight residual 1.532 1.512 0.020 9.60e-03 1.09e+04 4.34e+00 bond pdb=" C SER P 234 " pdb=" N PRO P 235 " ideal model delta sigma weight residual 1.334 1.378 -0.044 2.34e-02 1.83e+03 3.50e+00 bond pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " ideal model delta sigma weight residual 1.422 1.477 -0.055 3.00e-02 1.11e+03 3.39e+00 bond pdb=" C1' DC J 56 " pdb=" N1 DC J 56 " ideal model delta sigma weight residual 1.490 1.544 -0.054 3.00e-02 1.11e+03 3.19e+00 ... (remaining 15890 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 21713 1.41 - 2.81: 1051 2.81 - 4.22: 143 4.22 - 5.62: 19 5.62 - 7.03: 2 Bond angle restraints: 22928 Sorted by residual: angle pdb=" C2' DT I 161 " pdb=" C1' DT I 161 " pdb=" N1 DT I 161 " ideal model delta sigma weight residual 113.50 118.33 -4.83 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sigma weight residual 120.20 124.88 -4.68 1.50e+00 4.44e-01 9.72e+00 angle pdb=" C LYS O 264 " pdb=" CA LYS O 264 " pdb=" CB LYS O 264 " ideal model delta sigma weight residual 112.27 107.04 5.23 1.75e+00 3.27e-01 8.94e+00 angle pdb=" C2' DT J 54 " pdb=" C1' DT J 54 " pdb=" N1 DT J 54 " ideal model delta sigma weight residual 113.50 117.98 -4.48 1.50e+00 4.44e-01 8.94e+00 angle pdb=" C2' DC I 110 " pdb=" C1' DC I 110 " pdb=" N1 DC I 110 " ideal model delta sigma weight residual 113.50 117.85 -4.35 1.50e+00 4.44e-01 8.40e+00 ... (remaining 22923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.42: 7098 32.42 - 64.85: 1609 64.85 - 97.27: 46 97.27 - 129.69: 0 129.69 - 162.12: 2 Dihedral angle restraints: 8755 sinusoidal: 5893 harmonic: 2862 Sorted by residual: dihedral pdb=" CA LYS O 237 " pdb=" C LYS O 237 " pdb=" N PRO O 238 " pdb=" CA PRO O 238 " ideal model delta harmonic sigma weight residual 180.00 158.36 21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" C4' DG J 127 " pdb=" C3' DG J 127 " pdb=" O3' DG J 127 " pdb=" P DG J 128 " ideal model delta sinusoidal sigma weight residual 220.00 57.88 162.12 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DC J 93 " pdb=" C3' DC J 93 " pdb=" O3' DC J 93 " pdb=" P DC J 94 " ideal model delta sinusoidal sigma weight residual 220.00 73.49 146.51 1 3.50e+01 8.16e-04 1.44e+01 ... (remaining 8752 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1669 0.029 - 0.058: 546 0.058 - 0.087: 281 0.087 - 0.116: 55 0.116 - 0.144: 12 Chirality restraints: 2563 Sorted by residual: chirality pdb=" P DG J 128 " pdb=" OP1 DG J 128 " pdb=" OP2 DG J 128 " pdb=" O5' DG J 128 " both_signs ideal model delta sigma weight residual True 2.35 -2.49 -0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA ILE D 89 " pdb=" N ILE D 89 " pdb=" C ILE D 89 " pdb=" CB ILE D 89 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE C 79 " pdb=" N ILE C 79 " pdb=" C ILE C 79 " pdb=" CB ILE C 79 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 2560 not shown) Planarity restraints: 1719 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS P 237 " -0.062 5.00e-02 4.00e+02 9.44e-02 1.43e+01 pdb=" N PRO P 238 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO P 238 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO P 238 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 237 " -0.051 5.00e-02 4.00e+02 7.70e-02 9.48e+00 pdb=" N PRO O 238 " 0.133 5.00e-02 4.00e+02 pdb=" CA PRO O 238 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO O 238 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 140 " 0.032 2.00e-02 2.50e+03 1.60e-02 6.41e+00 pdb=" N1 DT I 140 " -0.036 2.00e-02 2.50e+03 pdb=" C2 DT I 140 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DT I 140 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT I 140 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DT I 140 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT I 140 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT I 140 " -0.000 2.00e-02 2.50e+03 pdb=" C7 DT I 140 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 140 " 0.001 2.00e-02 2.50e+03 ... (remaining 1716 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 183 2.63 - 3.20: 12511 3.20 - 3.77: 28290 3.77 - 4.33: 36387 4.33 - 4.90: 52114 Nonbonded interactions: 129485 Sorted by model distance: nonbonded pdb=" OP1 DA I 144 " pdb=" OG SER H 32 " model vdw 2.063 3.040 nonbonded pdb=" O THR G 76 " pdb=" OG1 THR H 52 " model vdw 2.073 3.040 nonbonded pdb=" OP1 DG J 143 " pdb=" OG1 THR A 45 " model vdw 2.189 3.040 nonbonded pdb=" O THR C 76 " pdb=" OG1 THR D 52 " model vdw 2.218 3.040 nonbonded pdb=" OE1 GLN F 27 " pdb=" NH1 ARG F 55 " model vdw 2.235 3.120 ... (remaining 129480 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 10 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 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: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.640 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.005 0.055 15895 Z= 0.245 Angle : 0.676 7.031 22928 Z= 0.423 Chirality : 0.037 0.144 2563 Planarity : 0.005 0.094 1719 Dihedral : 25.927 162.118 6911 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 1.78 Ramachandran Plot: Outliers : 0.31 % Allowed : 1.97 % Favored : 97.72 % Rotamer: Outliers : 1.20 % Allowed : 1.92 % Favored : 96.89 % 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: 3.06 (0.28), residues: 964 helix: 3.30 (0.21), residues: 622 sheet: -1.64 (0.94), residues: 24 loop : -0.35 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 214 HIS 0.002 0.001 HIS B 75 PHE 0.008 0.001 PHE P 224 TYR 0.007 0.001 TYR B 72 ARG 0.004 0.000 ARG O 265 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 450 time to evaluate : 1.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 204 PHE cc_start: 0.9280 (m-80) cc_final: 0.9021 (m-80) REVERT: O 260 LEU cc_start: 0.4439 (OUTLIER) cc_final: 0.3684 (tt) REVERT: P 175 TYR cc_start: 0.4490 (m-80) cc_final: 0.3490 (m-10) REVERT: G 23 LEU cc_start: 0.9433 (mt) cc_final: 0.9050 (mp) REVERT: G 24 GLN cc_start: 0.8694 (mm-40) cc_final: 0.8075 (mm-40) REVERT: G 34 LEU cc_start: 0.9645 (mt) cc_final: 0.9432 (mt) REVERT: G 50 TYR cc_start: 0.8592 (t80) cc_final: 0.8381 (t80) REVERT: G 83 LEU cc_start: 0.9576 (mt) cc_final: 0.9330 (mt) REVERT: G 87 ILE cc_start: 0.9571 (mt) cc_final: 0.9297 (tp) REVERT: G 88 ARG cc_start: 0.8798 (mmt180) cc_final: 0.8191 (mtp180) REVERT: G 100 VAL cc_start: 0.9270 (t) cc_final: 0.8998 (p) REVERT: A 50 GLU cc_start: 0.9388 (mt-10) cc_final: 0.8780 (mt-10) REVERT: A 51 ILE cc_start: 0.8280 (mt) cc_final: 0.7983 (mt) REVERT: A 54 TYR cc_start: 0.9282 (m-80) cc_final: 0.8637 (m-80) REVERT: A 92 LEU cc_start: 0.8900 (mt) cc_final: 0.8688 (mt) REVERT: A 101 VAL cc_start: 0.9237 (t) cc_final: 0.8984 (t) REVERT: A 105 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8503 (tm-30) REVERT: B 39 ARG cc_start: 0.9188 (mmt-90) cc_final: 0.8428 (tpp-160) REVERT: B 68 ASP cc_start: 0.8814 (m-30) cc_final: 0.8492 (m-30) REVERT: B 70 VAL cc_start: 0.9680 (t) cc_final: 0.9344 (m) REVERT: B 87 VAL cc_start: 0.9811 (t) cc_final: 0.9589 (t) REVERT: B 91 LYS cc_start: 0.9690 (ttpt) cc_final: 0.9213 (ptmm) REVERT: C 38 ASN cc_start: 0.8671 (m110) cc_final: 0.8297 (t0) REVERT: C 50 TYR cc_start: 0.8243 (t80) cc_final: 0.7998 (t80) REVERT: C 51 LEU cc_start: 0.9684 (tp) cc_final: 0.9477 (tp) REVERT: C 90 ASP cc_start: 0.8882 (t0) cc_final: 0.8573 (t0) REVERT: C 92 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8750 (mt-10) REVERT: D 62 MET cc_start: 0.9190 (mmm) cc_final: 0.8915 (mmm) REVERT: D 85 LYS cc_start: 0.9370 (mtpt) cc_final: 0.9059 (mmmt) REVERT: D 87 SER cc_start: 0.9418 (m) cc_final: 0.8534 (p) REVERT: D 89 ILE cc_start: 0.9390 (mt) cc_final: 0.9185 (tp) REVERT: E 48 LEU cc_start: 0.9319 (mt) cc_final: 0.8954 (mt) REVERT: E 60 LEU cc_start: 0.9209 (mt) cc_final: 0.8000 (mp) REVERT: E 73 GLU cc_start: 0.8970 (tt0) cc_final: 0.8589 (mt-10) REVERT: E 93 GLN cc_start: 0.9059 (tt0) cc_final: 0.8246 (tm-30) REVERT: E 106 ASP cc_start: 0.9057 (m-30) cc_final: 0.8590 (m-30) REVERT: E 109 LEU cc_start: 0.9646 (mt) cc_final: 0.9210 (mm) REVERT: E 125 GLN cc_start: 0.9266 (mt0) cc_final: 0.8876 (mp10) REVERT: F 58 LEU cc_start: 0.9659 (tp) cc_final: 0.9415 (tp) REVERT: F 68 ASP cc_start: 0.8909 (m-30) cc_final: 0.8691 (m-30) REVERT: F 85 ASP cc_start: 0.9098 (m-30) cc_final: 0.8795 (t0) REVERT: F 87 VAL cc_start: 0.9752 (t) cc_final: 0.9449 (t) REVERT: F 91 LYS cc_start: 0.9430 (ttpt) cc_final: 0.9149 (ptpt) REVERT: H 38 SER cc_start: 0.9131 (m) cc_final: 0.8652 (p) REVERT: H 68 ASP cc_start: 0.8760 (t0) cc_final: 0.8478 (t0) REVERT: H 90 THR cc_start: 0.8750 (p) cc_final: 0.8214 (p) REVERT: H 91 SER cc_start: 0.9118 (p) cc_final: 0.8914 (t) REVERT: H 93 GLU cc_start: 0.8666 (mp0) cc_final: 0.8332 (mp0) REVERT: H 113 GLU cc_start: 0.9315 (mm-30) cc_final: 0.9006 (mm-30) outliers start: 10 outliers final: 2 residues processed: 456 average time/residue: 0.3253 time to fit residues: 201.9871 Evaluate side-chains 295 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 292 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 108 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 0.6980 chunk 51 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.0170 chunk 116 optimal weight: 2.9990 overall best weight: 1.3222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 212 GLN ** O 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 215 GLN G 68 ASN G 89 ASN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 HIS B 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 63 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15895 Z= 0.217 Angle : 0.638 7.908 22928 Z= 0.378 Chirality : 0.037 0.197 2563 Planarity : 0.006 0.092 1719 Dihedral : 29.984 160.382 4918 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.07 % Favored : 97.61 % Rotamer: Outliers : 0.24 % Allowed : 3.23 % Favored : 96.53 % 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: 2.43 (0.27), residues: 964 helix: 2.63 (0.20), residues: 624 sheet: -1.83 (0.93), residues: 24 loop : -0.19 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP P 214 HIS 0.003 0.001 HIS D 49 PHE 0.014 0.002 PHE F 100 TYR 0.018 0.002 TYR G 39 ARG 0.011 0.001 ARG O 213 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 349 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 181 MET cc_start: 0.4457 (tpt) cc_final: 0.3633 (mmt) REVERT: G 34 LEU cc_start: 0.9622 (mt) cc_final: 0.9416 (mt) REVERT: G 58 LEU cc_start: 0.9688 (mm) cc_final: 0.9425 (mm) REVERT: G 64 GLU cc_start: 0.9496 (OUTLIER) cc_final: 0.8884 (pp20) REVERT: G 87 ILE cc_start: 0.9561 (mt) cc_final: 0.8985 (tp) REVERT: G 88 ARG cc_start: 0.8888 (mmt180) cc_final: 0.7826 (mtp180) REVERT: G 94 ASN cc_start: 0.9270 (t0) cc_final: 0.9005 (m-40) REVERT: G 100 VAL cc_start: 0.9282 (t) cc_final: 0.8980 (p) REVERT: A 50 GLU cc_start: 0.9426 (mt-10) cc_final: 0.8779 (mt-10) REVERT: A 51 ILE cc_start: 0.8345 (mt) cc_final: 0.8012 (mt) REVERT: A 53 ARG cc_start: 0.9662 (ptm-80) cc_final: 0.9398 (ptm160) REVERT: A 73 GLU cc_start: 0.8287 (tt0) cc_final: 0.7850 (tt0) REVERT: A 81 ASP cc_start: 0.7928 (t0) cc_final: 0.7699 (t0) REVERT: A 87 SER cc_start: 0.8886 (p) cc_final: 0.8411 (t) REVERT: A 90 MET cc_start: 0.8820 (mpp) cc_final: 0.8384 (mmm) REVERT: A 94 GLU cc_start: 0.8615 (mm-30) cc_final: 0.8400 (mm-30) REVERT: A 105 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8430 (tm-30) REVERT: A 126 LEU cc_start: 0.9530 (mm) cc_final: 0.9018 (mm) REVERT: B 25 ASN cc_start: 0.7932 (m110) cc_final: 0.7550 (m110) REVERT: B 39 ARG cc_start: 0.9238 (mmt-90) cc_final: 0.8629 (tpp-160) REVERT: B 49 LEU cc_start: 0.9530 (mm) cc_final: 0.9042 (tp) REVERT: B 84 MET cc_start: 0.9327 (mpp) cc_final: 0.9054 (mpp) REVERT: C 50 TYR cc_start: 0.8358 (t80) cc_final: 0.7835 (t80) REVERT: C 74 LYS cc_start: 0.9401 (mmtm) cc_final: 0.9111 (mmtm) REVERT: C 78 ILE cc_start: 0.8490 (mm) cc_final: 0.8224 (tp) REVERT: C 90 ASP cc_start: 0.8546 (t0) cc_final: 0.8302 (t0) REVERT: C 92 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8430 (mt-10) REVERT: D 62 MET cc_start: 0.9053 (mmm) cc_final: 0.8828 (mmm) REVERT: D 85 LYS cc_start: 0.9355 (mtpt) cc_final: 0.9075 (mmmt) REVERT: D 94 ILE cc_start: 0.9424 (OUTLIER) cc_final: 0.9146 (mt) REVERT: D 101 LEU cc_start: 0.9160 (tt) cc_final: 0.8866 (tt) REVERT: E 48 LEU cc_start: 0.9229 (mt) cc_final: 0.8907 (mt) REVERT: E 70 LEU cc_start: 0.9665 (tp) cc_final: 0.9426 (tp) REVERT: E 74 ILE cc_start: 0.9443 (mt) cc_final: 0.9162 (mt) REVERT: E 77 ASP cc_start: 0.9602 (m-30) cc_final: 0.9364 (m-30) REVERT: E 120 MET cc_start: 0.9019 (mmm) cc_final: 0.8630 (mmm) REVERT: F 44 LYS cc_start: 0.8956 (tptm) cc_final: 0.8614 (tptm) REVERT: F 63 GLU cc_start: 0.9333 (pt0) cc_final: 0.9060 (pp20) REVERT: F 84 MET cc_start: 0.9505 (tpt) cc_final: 0.9167 (tpp) REVERT: H 49 HIS cc_start: 0.8948 (m-70) cc_final: 0.8386 (m-70) REVERT: H 59 MET cc_start: 0.9024 (tpp) cc_final: 0.8786 (tpp) REVERT: H 68 ASP cc_start: 0.8868 (t0) cc_final: 0.8606 (t0) REVERT: H 69 ILE cc_start: 0.9111 (mm) cc_final: 0.8674 (mm) REVERT: H 86 ARG cc_start: 0.8996 (mmt-90) cc_final: 0.8450 (mmm-85) REVERT: H 91 SER cc_start: 0.9014 (p) cc_final: 0.8543 (p) REVERT: H 105 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8759 (mm-30) REVERT: H 109 HIS cc_start: 0.8870 (m-70) cc_final: 0.8204 (m90) REVERT: H 113 GLU cc_start: 0.9389 (mm-30) cc_final: 0.8974 (mm-30) outliers start: 2 outliers final: 0 residues processed: 350 average time/residue: 0.3045 time to fit residues: 149.1829 Evaluate side-chains 274 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 79 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 209 GLN ** O 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 215 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 82 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15895 Z= 0.246 Angle : 0.640 7.799 22928 Z= 0.380 Chirality : 0.037 0.184 2563 Planarity : 0.006 0.093 1719 Dihedral : 30.180 158.155 4918 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.39 % Favored : 97.30 % Rotamer: Outliers : 0.48 % Allowed : 3.95 % Favored : 95.57 % 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: 1.81 (0.27), residues: 964 helix: 2.09 (0.20), residues: 626 sheet: -1.73 (0.99), residues: 24 loop : -0.36 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP P 214 HIS 0.005 0.001 HIS B 75 PHE 0.015 0.002 PHE F 61 TYR 0.015 0.002 TYR G 50 ARG 0.006 0.001 ARG D 33 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 325 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.7838 (mpp) cc_final: 0.7454 (mpp) REVERT: P 181 MET cc_start: 0.4565 (tpt) cc_final: 0.3701 (mmt) REVERT: G 58 LEU cc_start: 0.9666 (mm) cc_final: 0.9330 (mm) REVERT: G 68 ASN cc_start: 0.9659 (m-40) cc_final: 0.9045 (m110) REVERT: G 87 ILE cc_start: 0.9581 (mt) cc_final: 0.9036 (tp) REVERT: A 51 ILE cc_start: 0.8235 (mt) cc_final: 0.7870 (mt) REVERT: A 53 ARG cc_start: 0.9527 (ptm-80) cc_final: 0.9246 (ptm160) REVERT: A 54 TYR cc_start: 0.9550 (m-80) cc_final: 0.8841 (m-80) REVERT: A 61 LEU cc_start: 0.8677 (mt) cc_final: 0.8254 (mt) REVERT: A 70 LEU cc_start: 0.9288 (tp) cc_final: 0.8714 (tp) REVERT: A 73 GLU cc_start: 0.8406 (tt0) cc_final: 0.8183 (pt0) REVERT: A 87 SER cc_start: 0.9063 (p) cc_final: 0.8551 (t) REVERT: A 90 MET cc_start: 0.8904 (mpp) cc_final: 0.8476 (mmm) REVERT: A 105 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8417 (tm-30) REVERT: A 130 ILE cc_start: 0.9505 (mm) cc_final: 0.9223 (mm) REVERT: B 39 ARG cc_start: 0.9052 (mmt-90) cc_final: 0.8691 (tpp-160) REVERT: B 49 LEU cc_start: 0.9525 (mm) cc_final: 0.9047 (tp) REVERT: B 84 MET cc_start: 0.9312 (mpp) cc_final: 0.9081 (mpp) REVERT: C 74 LYS cc_start: 0.9378 (mmtm) cc_final: 0.9116 (mmtm) REVERT: C 78 ILE cc_start: 0.8563 (mm) cc_final: 0.8354 (tp) REVERT: C 90 ASP cc_start: 0.8255 (t0) cc_final: 0.7932 (t0) REVERT: D 34 LYS cc_start: 0.8674 (pptt) cc_final: 0.8380 (mmtp) REVERT: D 62 MET cc_start: 0.9170 (mmm) cc_final: 0.8962 (mmm) REVERT: D 85 LYS cc_start: 0.9432 (mtpt) cc_final: 0.9136 (mmmt) REVERT: D 101 LEU cc_start: 0.9134 (tt) cc_final: 0.8883 (tt) REVERT: E 74 ILE cc_start: 0.9384 (mt) cc_final: 0.9178 (mt) REVERT: E 77 ASP cc_start: 0.9596 (m-30) cc_final: 0.9368 (m-30) REVERT: E 90 MET cc_start: 0.9430 (mmp) cc_final: 0.9194 (mmm) REVERT: E 93 GLN cc_start: 0.8892 (tt0) cc_final: 0.8676 (tt0) REVERT: E 120 MET cc_start: 0.8886 (mmm) cc_final: 0.8425 (mmm) REVERT: F 63 GLU cc_start: 0.9266 (pt0) cc_final: 0.8845 (pp20) REVERT: F 64 ASN cc_start: 0.9549 (t0) cc_final: 0.9271 (t0) REVERT: F 84 MET cc_start: 0.9497 (tpt) cc_final: 0.9071 (tpp) REVERT: H 46 LYS cc_start: 0.9421 (ptpp) cc_final: 0.8853 (ptpp) REVERT: H 47 GLN cc_start: 0.9207 (tm-30) cc_final: 0.8996 (tm-30) REVERT: H 49 HIS cc_start: 0.9054 (m-70) cc_final: 0.8754 (m90) REVERT: H 59 MET cc_start: 0.9080 (tpp) cc_final: 0.8767 (tpp) REVERT: H 63 ASN cc_start: 0.9337 (m-40) cc_final: 0.9124 (m110) REVERT: H 68 ASP cc_start: 0.8920 (t0) cc_final: 0.8712 (t0) REVERT: H 69 ILE cc_start: 0.8945 (mm) cc_final: 0.8534 (mm) REVERT: H 82 HIS cc_start: 0.8985 (OUTLIER) cc_final: 0.8587 (m90) REVERT: H 101 LEU cc_start: 0.9102 (mt) cc_final: 0.8862 (mt) REVERT: H 108 LYS cc_start: 0.9333 (ptmm) cc_final: 0.9106 (pttm) REVERT: H 109 HIS cc_start: 0.8920 (m-70) cc_final: 0.7972 (m-70) REVERT: H 113 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8660 (mm-30) outliers start: 4 outliers final: 0 residues processed: 328 average time/residue: 0.2960 time to fit residues: 136.1795 Evaluate side-chains 263 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 262 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 115 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 15895 Z= 0.303 Angle : 0.673 7.878 22928 Z= 0.397 Chirality : 0.038 0.188 2563 Planarity : 0.005 0.093 1719 Dihedral : 30.428 156.966 4918 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.31 % Allowed : 2.80 % Favored : 96.89 % Rotamer: Outliers : 0.24 % Allowed : 2.75 % Favored : 97.01 % 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: 1.46 (0.27), residues: 964 helix: 1.78 (0.20), residues: 630 sheet: -1.82 (0.94), residues: 24 loop : -0.43 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP P 244 HIS 0.010 0.002 HIS D 109 PHE 0.011 0.002 PHE P 224 TYR 0.018 0.002 TYR P 207 ARG 0.007 0.001 ARG C 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 301 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.7793 (mpp) cc_final: 0.7333 (mpp) REVERT: P 181 MET cc_start: 0.4183 (tpt) cc_final: 0.3424 (mmt) REVERT: P 201 MET cc_start: -0.0253 (mmt) cc_final: -0.0611 (mmt) REVERT: G 38 ASN cc_start: 0.9234 (t0) cc_final: 0.9030 (t0) REVERT: G 56 GLU cc_start: 0.9063 (tm-30) cc_final: 0.8859 (tm-30) REVERT: G 88 ARG cc_start: 0.8739 (mmt180) cc_final: 0.7748 (mtp180) REVERT: A 51 ILE cc_start: 0.8458 (mt) cc_final: 0.8130 (mt) REVERT: A 53 ARG cc_start: 0.9534 (ptm-80) cc_final: 0.9272 (ptm160) REVERT: A 54 TYR cc_start: 0.9537 (m-80) cc_final: 0.8750 (m-80) REVERT: A 70 LEU cc_start: 0.9367 (tp) cc_final: 0.8883 (tt) REVERT: A 73 GLU cc_start: 0.8266 (tt0) cc_final: 0.7961 (pt0) REVERT: A 87 SER cc_start: 0.9031 (p) cc_final: 0.8455 (t) REVERT: A 90 MET cc_start: 0.8950 (mpp) cc_final: 0.8725 (mpp) REVERT: A 105 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8385 (tm-30) REVERT: A 130 ILE cc_start: 0.9529 (mm) cc_final: 0.9261 (mm) REVERT: B 39 ARG cc_start: 0.9021 (mmt-90) cc_final: 0.8540 (tpp-160) REVERT: B 43 VAL cc_start: 0.9170 (t) cc_final: 0.8793 (p) REVERT: B 49 LEU cc_start: 0.9511 (mm) cc_final: 0.9031 (tp) REVERT: B 63 GLU cc_start: 0.8731 (pp20) cc_final: 0.8466 (pp20) REVERT: B 84 MET cc_start: 0.9393 (mpp) cc_final: 0.9105 (mpp) REVERT: C 74 LYS cc_start: 0.9366 (mmtm) cc_final: 0.9113 (mmtm) REVERT: C 78 ILE cc_start: 0.8470 (mm) cc_final: 0.8205 (tp) REVERT: C 90 ASP cc_start: 0.8471 (t0) cc_final: 0.8243 (t0) REVERT: D 34 LYS cc_start: 0.8669 (pptt) cc_final: 0.8260 (mmtp) REVERT: D 62 MET cc_start: 0.9165 (mmm) cc_final: 0.8708 (mmm) REVERT: D 76 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8817 (mm-30) REVERT: D 101 LEU cc_start: 0.9226 (tt) cc_final: 0.8962 (tt) REVERT: E 60 LEU cc_start: 0.9267 (mm) cc_final: 0.8944 (mm) REVERT: E 71 VAL cc_start: 0.9676 (t) cc_final: 0.9471 (p) REVERT: E 74 ILE cc_start: 0.9403 (mt) cc_final: 0.9202 (mt) REVERT: E 77 ASP cc_start: 0.9578 (m-30) cc_final: 0.9314 (m-30) REVERT: E 82 LEU cc_start: 0.7827 (mt) cc_final: 0.7465 (mt) REVERT: E 90 MET cc_start: 0.9416 (mmp) cc_final: 0.9185 (mmm) REVERT: E 93 GLN cc_start: 0.9008 (tt0) cc_final: 0.8696 (tt0) REVERT: E 119 ILE cc_start: 0.9482 (pt) cc_final: 0.9243 (pt) REVERT: E 120 MET cc_start: 0.9081 (mmm) cc_final: 0.8537 (mmm) REVERT: E 126 LEU cc_start: 0.9212 (tp) cc_final: 0.8974 (mm) REVERT: F 63 GLU cc_start: 0.9311 (pt0) cc_final: 0.8913 (pp20) REVERT: F 64 ASN cc_start: 0.9598 (t0) cc_final: 0.9273 (t0) REVERT: F 84 MET cc_start: 0.9522 (tpt) cc_final: 0.9172 (tpp) REVERT: F 88 TYR cc_start: 0.9111 (m-10) cc_final: 0.8679 (m-80) REVERT: F 91 LYS cc_start: 0.9458 (ttpt) cc_final: 0.9223 (mtmt) REVERT: H 46 LYS cc_start: 0.9494 (ptpp) cc_final: 0.8917 (ptpp) REVERT: H 47 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8952 (tm-30) REVERT: H 49 HIS cc_start: 0.9049 (m-70) cc_final: 0.8787 (m90) REVERT: H 59 MET cc_start: 0.9089 (tpp) cc_final: 0.8617 (tpp) REVERT: H 69 ILE cc_start: 0.9071 (mm) cc_final: 0.8858 (mm) REVERT: H 109 HIS cc_start: 0.9004 (m-70) cc_final: 0.8075 (m-70) REVERT: H 113 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8629 (mm-30) outliers start: 2 outliers final: 1 residues processed: 301 average time/residue: 0.3116 time to fit residues: 133.3450 Evaluate side-chains 252 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 251 time to evaluate : 1.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 92 optimal weight: 0.6980 chunk 51 optimal weight: 9.9990 chunk 105 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 111 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 215 GLN G 68 ASN ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15895 Z= 0.223 Angle : 0.635 8.106 22928 Z= 0.376 Chirality : 0.037 0.196 2563 Planarity : 0.005 0.094 1719 Dihedral : 30.395 152.977 4918 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.59 % Favored : 97.20 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % 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: 1.43 (0.27), residues: 964 helix: 1.75 (0.20), residues: 630 sheet: -1.84 (0.96), residues: 24 loop : -0.45 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP P 214 HIS 0.005 0.001 HIS F 75 PHE 0.011 0.001 PHE E 67 TYR 0.019 0.002 TYR H 40 ARG 0.007 0.001 ARG H 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 311 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.7789 (mpp) cc_final: 0.7243 (mpp) REVERT: P 175 TYR cc_start: 0.3868 (m-80) cc_final: 0.3636 (m-80) REVERT: P 181 MET cc_start: 0.4382 (tpt) cc_final: 0.3646 (mmt) REVERT: G 38 ASN cc_start: 0.9218 (t0) cc_final: 0.8960 (t0) REVERT: G 56 GLU cc_start: 0.9010 (tm-30) cc_final: 0.8720 (tm-30) REVERT: G 61 GLU cc_start: 0.8946 (tp30) cc_final: 0.8666 (tp30) REVERT: G 68 ASN cc_start: 0.9506 (m-40) cc_final: 0.9200 (m110) REVERT: A 50 GLU cc_start: 0.9468 (mt-10) cc_final: 0.8665 (mt-10) REVERT: A 53 ARG cc_start: 0.9511 (ptm-80) cc_final: 0.9277 (ptm160) REVERT: A 54 TYR cc_start: 0.9501 (m-80) cc_final: 0.8929 (m-80) REVERT: A 70 LEU cc_start: 0.9292 (tp) cc_final: 0.8711 (tp) REVERT: A 73 GLU cc_start: 0.8246 (tt0) cc_final: 0.7902 (pt0) REVERT: A 87 SER cc_start: 0.9043 (p) cc_final: 0.8500 (t) REVERT: A 90 MET cc_start: 0.8985 (mpp) cc_final: 0.8564 (mmm) REVERT: A 105 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8368 (tm-30) REVERT: A 120 MET cc_start: 0.8485 (mmt) cc_final: 0.8269 (mmt) REVERT: A 130 ILE cc_start: 0.9506 (mm) cc_final: 0.9276 (mm) REVERT: B 31 LYS cc_start: 0.9470 (tmtt) cc_final: 0.9180 (tmtt) REVERT: B 39 ARG cc_start: 0.8924 (mmt-90) cc_final: 0.7891 (tpp-160) REVERT: B 43 VAL cc_start: 0.9079 (t) cc_final: 0.8743 (p) REVERT: B 49 LEU cc_start: 0.9545 (mm) cc_final: 0.9049 (tp) REVERT: B 63 GLU cc_start: 0.8761 (pp20) cc_final: 0.8489 (pp20) REVERT: B 84 MET cc_start: 0.9251 (mpp) cc_final: 0.9029 (mmm) REVERT: C 39 TYR cc_start: 0.8959 (m-80) cc_final: 0.8167 (m-80) REVERT: C 74 LYS cc_start: 0.9355 (mmtm) cc_final: 0.9098 (mppt) REVERT: C 89 ASN cc_start: 0.8396 (p0) cc_final: 0.8184 (p0) REVERT: D 34 LYS cc_start: 0.8845 (pptt) cc_final: 0.8363 (mmtp) REVERT: D 68 ASP cc_start: 0.9340 (t0) cc_final: 0.9068 (t0) REVERT: D 96 THR cc_start: 0.9560 (m) cc_final: 0.9296 (p) REVERT: D 101 LEU cc_start: 0.9264 (tt) cc_final: 0.8949 (tt) REVERT: E 48 LEU cc_start: 0.9379 (mt) cc_final: 0.9159 (mt) REVERT: E 60 LEU cc_start: 0.9229 (mm) cc_final: 0.8965 (mm) REVERT: E 73 GLU cc_start: 0.9320 (pt0) cc_final: 0.8781 (pt0) REVERT: E 77 ASP cc_start: 0.9536 (m-30) cc_final: 0.9239 (m-30) REVERT: E 82 LEU cc_start: 0.7818 (mt) cc_final: 0.7275 (mt) REVERT: E 90 MET cc_start: 0.9396 (mmp) cc_final: 0.9173 (mmm) REVERT: E 120 MET cc_start: 0.8981 (mmm) cc_final: 0.8480 (mmm) REVERT: F 25 ASN cc_start: 0.8488 (m-40) cc_final: 0.8234 (m-40) REVERT: F 44 LYS cc_start: 0.8892 (tptm) cc_final: 0.8589 (tppt) REVERT: F 63 GLU cc_start: 0.9301 (pt0) cc_final: 0.8876 (pp20) REVERT: F 64 ASN cc_start: 0.9612 (t0) cc_final: 0.9297 (t0) REVERT: F 84 MET cc_start: 0.9324 (tpt) cc_final: 0.9038 (tpp) REVERT: H 46 LYS cc_start: 0.9568 (ptpp) cc_final: 0.9337 (mmtt) REVERT: H 47 GLN cc_start: 0.9242 (tm-30) cc_final: 0.8885 (tm-30) REVERT: H 49 HIS cc_start: 0.8974 (m-70) cc_final: 0.8668 (m-70) REVERT: H 69 ILE cc_start: 0.9028 (mm) cc_final: 0.8609 (mm) REVERT: H 109 HIS cc_start: 0.8973 (m-70) cc_final: 0.8099 (m-70) REVERT: H 113 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8578 (mm-30) outliers start: 0 outliers final: 0 residues processed: 311 average time/residue: 0.2995 time to fit residues: 130.4732 Evaluate side-chains 258 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 258 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 chunk 24 optimal weight: 8.9990 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 30.0000 chunk 40 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 15895 Z= 0.371 Angle : 0.729 8.096 22928 Z= 0.427 Chirality : 0.040 0.177 2563 Planarity : 0.006 0.095 1719 Dihedral : 30.780 156.079 4918 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 19.47 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.63 % Favored : 96.16 % Rotamer: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.27), residues: 964 helix: 1.43 (0.20), residues: 626 sheet: -2.23 (0.92), residues: 24 loop : -0.65 (0.36), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP P 244 HIS 0.006 0.002 HIS G 124 PHE 0.024 0.002 PHE F 61 TYR 0.021 0.002 TYR P 207 ARG 0.017 0.001 ARG O 219 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 197 TYR cc_start: 0.8526 (m-10) cc_final: 0.8268 (m-10) REVERT: O 201 MET cc_start: 0.7786 (mpp) cc_final: 0.7428 (mpp) REVERT: P 181 MET cc_start: 0.4726 (tpt) cc_final: 0.4007 (mmt) REVERT: G 38 ASN cc_start: 0.9191 (t0) cc_final: 0.8922 (t0) REVERT: G 61 GLU cc_start: 0.8910 (tp30) cc_final: 0.8580 (tp30) REVERT: G 68 ASN cc_start: 0.9566 (m-40) cc_final: 0.9340 (m110) REVERT: A 50 GLU cc_start: 0.9472 (mt-10) cc_final: 0.9061 (tt0) REVERT: A 53 ARG cc_start: 0.9578 (ptm-80) cc_final: 0.9258 (ptm160) REVERT: A 54 TYR cc_start: 0.9480 (m-80) cc_final: 0.8376 (m-80) REVERT: A 73 GLU cc_start: 0.8114 (tt0) cc_final: 0.7896 (tt0) REVERT: A 87 SER cc_start: 0.9144 (p) cc_final: 0.8784 (p) REVERT: A 90 MET cc_start: 0.9037 (mpp) cc_final: 0.8704 (mmm) REVERT: A 105 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8294 (tm-30) REVERT: B 31 LYS cc_start: 0.9443 (tmtt) cc_final: 0.9127 (tmtt) REVERT: B 43 VAL cc_start: 0.9337 (t) cc_final: 0.8958 (p) REVERT: B 45 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8745 (mmm160) REVERT: B 49 LEU cc_start: 0.9491 (mm) cc_final: 0.8982 (tp) REVERT: B 63 GLU cc_start: 0.8800 (pp20) cc_final: 0.8543 (pp20) REVERT: B 64 ASN cc_start: 0.8896 (t0) cc_final: 0.8651 (t0) REVERT: B 84 MET cc_start: 0.9400 (mpp) cc_final: 0.9096 (mpp) REVERT: B 93 GLN cc_start: 0.8345 (pp30) cc_final: 0.7750 (pp30) REVERT: C 74 LYS cc_start: 0.9362 (mmtm) cc_final: 0.9110 (mppt) REVERT: C 90 ASP cc_start: 0.8572 (t0) cc_final: 0.8351 (t0) REVERT: D 34 LYS cc_start: 0.8844 (pptt) cc_final: 0.8432 (mmtp) REVERT: D 62 MET cc_start: 0.9241 (mmm) cc_final: 0.9012 (mmm) REVERT: D 85 LYS cc_start: 0.9493 (mtpt) cc_final: 0.8995 (mmmt) REVERT: D 96 THR cc_start: 0.9635 (m) cc_final: 0.9395 (p) REVERT: D 101 LEU cc_start: 0.9256 (tt) cc_final: 0.9012 (tt) REVERT: D 102 LEU cc_start: 0.8843 (mt) cc_final: 0.8642 (mt) REVERT: E 50 GLU cc_start: 0.8784 (tp30) cc_final: 0.8350 (tp30) REVERT: E 60 LEU cc_start: 0.9209 (mm) cc_final: 0.8923 (mm) REVERT: E 74 ILE cc_start: 0.9440 (mt) cc_final: 0.9200 (mt) REVERT: E 77 ASP cc_start: 0.9553 (m-30) cc_final: 0.9266 (m-30) REVERT: E 93 GLN cc_start: 0.9009 (tt0) cc_final: 0.8601 (tt0) REVERT: E 119 ILE cc_start: 0.9449 (pt) cc_final: 0.9209 (pt) REVERT: E 120 MET cc_start: 0.9057 (mmm) cc_final: 0.8574 (mmm) REVERT: F 60 VAL cc_start: 0.9537 (t) cc_final: 0.9221 (t) REVERT: F 63 GLU cc_start: 0.9317 (pt0) cc_final: 0.8876 (pp20) REVERT: F 64 ASN cc_start: 0.9633 (t0) cc_final: 0.9342 (t0) REVERT: F 84 MET cc_start: 0.9362 (tpt) cc_final: 0.8904 (tpp) REVERT: H 46 LYS cc_start: 0.9649 (ptpp) cc_final: 0.9394 (mmtt) REVERT: H 47 GLN cc_start: 0.9273 (tm-30) cc_final: 0.8947 (tm-30) REVERT: H 59 MET cc_start: 0.8973 (tpp) cc_final: 0.8301 (tpp) REVERT: H 68 ASP cc_start: 0.8835 (t0) cc_final: 0.8590 (t0) REVERT: H 69 ILE cc_start: 0.9092 (mm) cc_final: 0.8635 (mm) REVERT: H 72 ARG cc_start: 0.9085 (mtt180) cc_final: 0.8585 (mmm-85) REVERT: H 76 GLU cc_start: 0.8963 (mp0) cc_final: 0.8328 (mp0) REVERT: H 86 ARG cc_start: 0.8994 (mmt-90) cc_final: 0.8770 (tpp80) REVERT: H 109 HIS cc_start: 0.9041 (m-70) cc_final: 0.8089 (m170) REVERT: H 113 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8578 (mm-30) outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 0.3020 time to fit residues: 118.5315 Evaluate side-chains 250 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 250 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 119 optimal weight: 0.0980 chunk 13 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 123 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.5276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15895 Z= 0.195 Angle : 0.647 8.519 22928 Z= 0.379 Chirality : 0.037 0.179 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.561 150.876 4918 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.70 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % 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: 1.22 (0.27), residues: 964 helix: 1.59 (0.20), residues: 630 sheet: -1.73 (0.95), residues: 24 loop : -0.55 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP O 214 HIS 0.004 0.001 HIS P 220 PHE 0.013 0.001 PHE E 67 TYR 0.021 0.002 TYR H 40 ARG 0.009 0.000 ARG O 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 305 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 197 TYR cc_start: 0.8640 (m-10) cc_final: 0.8410 (m-10) REVERT: P 181 MET cc_start: 0.4384 (tpt) cc_final: 0.3754 (mmt) REVERT: G 61 GLU cc_start: 0.8899 (tp30) cc_final: 0.8472 (tp30) REVERT: G 64 GLU cc_start: 0.9105 (pp20) cc_final: 0.8778 (pp20) REVERT: G 68 ASN cc_start: 0.9525 (m-40) cc_final: 0.9207 (m110) REVERT: A 50 GLU cc_start: 0.9474 (mt-10) cc_final: 0.9026 (mt-10) REVERT: A 53 ARG cc_start: 0.9519 (ptm-80) cc_final: 0.9277 (ptm160) REVERT: A 54 TYR cc_start: 0.9479 (m-80) cc_final: 0.8977 (m-80) REVERT: A 87 SER cc_start: 0.8986 (p) cc_final: 0.8509 (t) REVERT: A 90 MET cc_start: 0.9015 (mpp) cc_final: 0.8724 (mpp) REVERT: A 94 GLU cc_start: 0.8768 (mm-30) cc_final: 0.8249 (mt-10) REVERT: A 105 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8298 (tm-30) REVERT: A 120 MET cc_start: 0.8560 (mmt) cc_final: 0.8033 (mmm) REVERT: A 126 LEU cc_start: 0.9568 (mm) cc_final: 0.9179 (mm) REVERT: A 130 ILE cc_start: 0.9467 (mm) cc_final: 0.9223 (mm) REVERT: B 43 VAL cc_start: 0.9222 (t) cc_final: 0.8848 (p) REVERT: B 45 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8621 (mmm160) REVERT: B 49 LEU cc_start: 0.9499 (mm) cc_final: 0.9025 (tp) REVERT: B 63 GLU cc_start: 0.8761 (pp20) cc_final: 0.8488 (pp20) REVERT: B 84 MET cc_start: 0.9102 (mpp) cc_final: 0.8865 (mmm) REVERT: C 36 LYS cc_start: 0.9382 (mmtm) cc_final: 0.9048 (mtmt) REVERT: C 74 LYS cc_start: 0.9334 (mmtm) cc_final: 0.9096 (mppt) REVERT: C 84 GLN cc_start: 0.9190 (tp-100) cc_final: 0.8984 (tp-100) REVERT: C 90 ASP cc_start: 0.8455 (t0) cc_final: 0.8209 (t0) REVERT: D 34 LYS cc_start: 0.8736 (pptt) cc_final: 0.8413 (mmtp) REVERT: D 85 LYS cc_start: 0.9457 (mtpt) cc_final: 0.8976 (mmmt) REVERT: D 96 THR cc_start: 0.9578 (m) cc_final: 0.9326 (p) REVERT: D 101 LEU cc_start: 0.9188 (tt) cc_final: 0.8970 (tt) REVERT: D 102 LEU cc_start: 0.8466 (mt) cc_final: 0.8245 (mp) REVERT: D 113 GLU cc_start: 0.9336 (tp30) cc_final: 0.9060 (tp30) REVERT: E 50 GLU cc_start: 0.8848 (tp30) cc_final: 0.8263 (tp30) REVERT: E 73 GLU cc_start: 0.9166 (pt0) cc_final: 0.8628 (pt0) REVERT: E 77 ASP cc_start: 0.9529 (m-30) cc_final: 0.9254 (m-30) REVERT: E 90 MET cc_start: 0.9297 (mmp) cc_final: 0.9091 (mmm) REVERT: E 93 GLN cc_start: 0.8972 (tt0) cc_final: 0.8648 (tt0) REVERT: E 105 GLU cc_start: 0.8785 (pp20) cc_final: 0.8468 (pp20) REVERT: E 106 ASP cc_start: 0.9074 (m-30) cc_final: 0.8798 (m-30) REVERT: E 119 ILE cc_start: 0.9422 (pt) cc_final: 0.9185 (pt) REVERT: E 120 MET cc_start: 0.9005 (mmm) cc_final: 0.8427 (mmm) REVERT: F 25 ASN cc_start: 0.8438 (m-40) cc_final: 0.8152 (m-40) REVERT: F 63 GLU cc_start: 0.9296 (pt0) cc_final: 0.8858 (pp20) REVERT: F 64 ASN cc_start: 0.9595 (t0) cc_final: 0.9272 (t0) REVERT: F 84 MET cc_start: 0.9233 (tpt) cc_final: 0.8946 (tpp) REVERT: H 34 LYS cc_start: 0.9211 (mmmm) cc_final: 0.8890 (mptt) REVERT: H 42 TYR cc_start: 0.7312 (t80) cc_final: 0.7041 (t80) REVERT: H 46 LYS cc_start: 0.9573 (ptpp) cc_final: 0.9125 (pttm) REVERT: H 59 MET cc_start: 0.8972 (tpp) cc_final: 0.8553 (tpp) REVERT: H 69 ILE cc_start: 0.8994 (mm) cc_final: 0.8601 (mm) REVERT: H 109 HIS cc_start: 0.8972 (m-70) cc_final: 0.8107 (m-70) REVERT: H 113 GLU cc_start: 0.9053 (mm-30) cc_final: 0.8495 (mm-30) REVERT: H 116 LYS cc_start: 0.9136 (pttm) cc_final: 0.8906 (pttm) outliers start: 0 outliers final: 0 residues processed: 305 average time/residue: 0.3057 time to fit residues: 129.6761 Evaluate side-chains 254 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 254 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 49 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 23 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 20.0000 chunk 96 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.5644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 15895 Z= 0.289 Angle : 0.689 8.648 22928 Z= 0.405 Chirality : 0.039 0.188 2563 Planarity : 0.006 0.095 1719 Dihedral : 30.639 152.224 4918 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.05 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: 1.01 (0.27), residues: 964 helix: 1.41 (0.20), residues: 626 sheet: -1.75 (0.98), residues: 24 loop : -0.55 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP P 244 HIS 0.011 0.002 HIS P 220 PHE 0.017 0.002 PHE D 65 TYR 0.025 0.002 TYR B 88 ARG 0.009 0.001 ARG O 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.7636 (mpp) cc_final: 0.7291 (mpp) REVERT: P 181 MET cc_start: 0.4682 (tpt) cc_final: 0.3990 (mmt) REVERT: G 61 GLU cc_start: 0.8875 (tp30) cc_final: 0.8362 (tp30) REVERT: G 64 GLU cc_start: 0.9120 (pp20) cc_final: 0.8684 (pp20) REVERT: G 68 ASN cc_start: 0.9547 (m-40) cc_final: 0.9218 (m110) REVERT: A 53 ARG cc_start: 0.9564 (ptm-80) cc_final: 0.9247 (ptm160) REVERT: A 54 TYR cc_start: 0.9435 (m-80) cc_final: 0.8948 (m-80) REVERT: A 87 SER cc_start: 0.9166 (p) cc_final: 0.8635 (t) REVERT: A 90 MET cc_start: 0.9065 (mpp) cc_final: 0.8807 (mpp) REVERT: A 94 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8111 (mt-10) REVERT: A 120 MET cc_start: 0.8510 (mmt) cc_final: 0.8054 (mmm) REVERT: B 31 LYS cc_start: 0.9403 (tmtt) cc_final: 0.9099 (tmtt) REVERT: B 43 VAL cc_start: 0.9317 (t) cc_final: 0.8961 (p) REVERT: B 49 LEU cc_start: 0.9474 (mm) cc_final: 0.8994 (tp) REVERT: B 63 GLU cc_start: 0.8817 (pp20) cc_final: 0.8551 (pp20) REVERT: B 64 ASN cc_start: 0.8931 (t0) cc_final: 0.8728 (t0) REVERT: C 74 LYS cc_start: 0.9301 (mmtm) cc_final: 0.9081 (mppt) REVERT: C 84 GLN cc_start: 0.9262 (tp-100) cc_final: 0.9028 (tp-100) REVERT: C 90 ASP cc_start: 0.8463 (t0) cc_final: 0.8161 (t0) REVERT: D 34 LYS cc_start: 0.8811 (pptt) cc_final: 0.8434 (mmtp) REVERT: D 62 MET cc_start: 0.9111 (mmm) cc_final: 0.8837 (mmm) REVERT: D 76 GLU cc_start: 0.9323 (mm-30) cc_final: 0.9018 (mm-30) REVERT: D 85 LYS cc_start: 0.9486 (mtpt) cc_final: 0.9042 (mmmt) REVERT: D 101 LEU cc_start: 0.9215 (tt) cc_final: 0.8813 (tt) REVERT: E 50 GLU cc_start: 0.8794 (tp30) cc_final: 0.8231 (tp30) REVERT: E 77 ASP cc_start: 0.9538 (m-30) cc_final: 0.9270 (m-30) REVERT: E 82 LEU cc_start: 0.8473 (mt) cc_final: 0.8135 (mt) REVERT: E 93 GLN cc_start: 0.9032 (tt0) cc_final: 0.8665 (tt0) REVERT: E 106 ASP cc_start: 0.9090 (m-30) cc_final: 0.8668 (m-30) REVERT: E 120 MET cc_start: 0.9001 (mmm) cc_final: 0.8523 (mmm) REVERT: F 49 LEU cc_start: 0.9466 (mt) cc_final: 0.9259 (mt) REVERT: F 63 GLU cc_start: 0.9297 (pt0) cc_final: 0.8842 (pp20) REVERT: F 64 ASN cc_start: 0.9645 (t0) cc_final: 0.9343 (t0) REVERT: F 84 MET cc_start: 0.9310 (tpt) cc_final: 0.8977 (tpp) REVERT: H 46 LYS cc_start: 0.9639 (ptpp) cc_final: 0.9396 (mmtt) REVERT: H 47 GLN cc_start: 0.9299 (tm-30) cc_final: 0.9097 (tm-30) REVERT: H 59 MET cc_start: 0.8928 (tpp) cc_final: 0.8685 (tpp) REVERT: H 68 ASP cc_start: 0.8883 (t0) cc_final: 0.8597 (t0) REVERT: H 69 ILE cc_start: 0.9023 (mm) cc_final: 0.8541 (mm) REVERT: H 72 ARG cc_start: 0.9058 (mtt180) cc_final: 0.8749 (mmm-85) REVERT: H 109 HIS cc_start: 0.8986 (m-70) cc_final: 0.8111 (m-70) REVERT: H 113 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8507 (mm-30) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.2938 time to fit residues: 120.8858 Evaluate side-chains 247 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 247 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 118 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 114 optimal weight: 7.9990 chunk 69 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 15895 Z= 0.215 Angle : 0.667 8.847 22928 Z= 0.388 Chirality : 0.037 0.190 2563 Planarity : 0.005 0.095 1719 Dihedral : 30.532 151.299 4918 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.84 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % 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: 1.09 (0.27), residues: 964 helix: 1.48 (0.20), residues: 626 sheet: -1.61 (1.01), residues: 24 loop : -0.56 (0.37), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 214 HIS 0.004 0.001 HIS B 75 PHE 0.012 0.001 PHE D 65 TYR 0.023 0.002 TYR H 40 ARG 0.009 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.7677 (mpp) cc_final: 0.7232 (mpp) REVERT: P 181 MET cc_start: 0.4692 (tpt) cc_final: 0.3990 (mmt) REVERT: G 61 GLU cc_start: 0.8862 (tp30) cc_final: 0.8388 (tp30) REVERT: G 64 GLU cc_start: 0.9095 (pp20) cc_final: 0.8636 (pp20) REVERT: G 68 ASN cc_start: 0.9518 (m-40) cc_final: 0.9121 (m110) REVERT: A 50 GLU cc_start: 0.9479 (mt-10) cc_final: 0.9027 (mt-10) REVERT: A 53 ARG cc_start: 0.9525 (ptm-80) cc_final: 0.9275 (ptm160) REVERT: A 54 TYR cc_start: 0.9477 (m-80) cc_final: 0.9047 (m-80) REVERT: A 87 SER cc_start: 0.9005 (p) cc_final: 0.8492 (t) REVERT: A 90 MET cc_start: 0.9073 (mpp) cc_final: 0.8703 (mmm) REVERT: A 94 GLU cc_start: 0.8762 (mm-30) cc_final: 0.8039 (mt-10) REVERT: A 120 MET cc_start: 0.8568 (mmt) cc_final: 0.7958 (mmm) REVERT: B 31 LYS cc_start: 0.9408 (tmtt) cc_final: 0.9088 (tmtt) REVERT: B 43 VAL cc_start: 0.9271 (t) cc_final: 0.8894 (p) REVERT: B 49 LEU cc_start: 0.9486 (mm) cc_final: 0.9025 (tp) REVERT: B 63 GLU cc_start: 0.8788 (pp20) cc_final: 0.8523 (pp20) REVERT: B 84 MET cc_start: 0.9305 (mpp) cc_final: 0.8840 (mmm) REVERT: C 36 LYS cc_start: 0.9358 (mmtm) cc_final: 0.9118 (mtmt) REVERT: C 74 LYS cc_start: 0.9288 (mmtm) cc_final: 0.9056 (mppt) REVERT: C 84 GLN cc_start: 0.9227 (tp-100) cc_final: 0.9001 (tp-100) REVERT: C 90 ASP cc_start: 0.8420 (t0) cc_final: 0.8129 (t0) REVERT: D 34 LYS cc_start: 0.8682 (pptt) cc_final: 0.8356 (mmtp) REVERT: D 76 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8918 (mm-30) REVERT: D 83 TYR cc_start: 0.8457 (m-10) cc_final: 0.7941 (m-10) REVERT: D 85 LYS cc_start: 0.9498 (mtpt) cc_final: 0.9088 (mmmt) REVERT: D 101 LEU cc_start: 0.9209 (tt) cc_final: 0.8902 (tt) REVERT: E 50 GLU cc_start: 0.8794 (tp30) cc_final: 0.8192 (tp30) REVERT: E 73 GLU cc_start: 0.9178 (pt0) cc_final: 0.8675 (pt0) REVERT: E 77 ASP cc_start: 0.9517 (m-30) cc_final: 0.9249 (m-30) REVERT: E 106 ASP cc_start: 0.9028 (m-30) cc_final: 0.8559 (m-30) REVERT: E 119 ILE cc_start: 0.9482 (pt) cc_final: 0.9270 (pt) REVERT: E 120 MET cc_start: 0.8972 (mmm) cc_final: 0.8439 (mmm) REVERT: F 25 ASN cc_start: 0.8216 (m-40) cc_final: 0.7881 (m-40) REVERT: F 49 LEU cc_start: 0.9445 (mt) cc_final: 0.9197 (mt) REVERT: F 63 GLU cc_start: 0.9318 (pt0) cc_final: 0.8911 (pp20) REVERT: F 64 ASN cc_start: 0.9616 (t0) cc_final: 0.9329 (t0) REVERT: F 84 MET cc_start: 0.9235 (tpt) cc_final: 0.8966 (tpp) REVERT: H 34 LYS cc_start: 0.9266 (mmmm) cc_final: 0.8962 (mptt) REVERT: H 42 TYR cc_start: 0.7326 (t80) cc_final: 0.7048 (t80) REVERT: H 46 LYS cc_start: 0.9605 (ptpp) cc_final: 0.9244 (pttm) REVERT: H 69 ILE cc_start: 0.9020 (mm) cc_final: 0.8622 (mm) REVERT: H 109 HIS cc_start: 0.8951 (m-70) cc_final: 0.8128 (m-70) REVERT: H 113 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8524 (mm-30) REVERT: H 116 LYS cc_start: 0.9141 (pttm) cc_final: 0.8934 (pttm) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.2965 time to fit residues: 123.6058 Evaluate side-chains 245 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 245 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 78 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 15895 Z= 0.194 Angle : 0.657 8.530 22928 Z= 0.383 Chirality : 0.037 0.180 2563 Planarity : 0.005 0.096 1719 Dihedral : 30.384 150.660 4918 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.53 % Favored : 96.27 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 964 helix: 1.38 (0.20), residues: 623 sheet: -1.58 (1.05), residues: 24 loop : -0.65 (0.36), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP O 214 HIS 0.004 0.001 HIS B 75 PHE 0.014 0.001 PHE D 65 TYR 0.024 0.002 TYR H 40 ARG 0.009 0.000 ARG B 45 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 201 MET cc_start: 0.8009 (mpp) cc_final: 0.7608 (mpp) REVERT: P 181 MET cc_start: 0.5057 (tpt) cc_final: 0.4247 (mmt) REVERT: P 245 THR cc_start: 0.7401 (p) cc_final: 0.7055 (p) REVERT: G 61 GLU cc_start: 0.8753 (tp30) cc_final: 0.8336 (tp30) REVERT: G 64 GLU cc_start: 0.9066 (pp20) cc_final: 0.8652 (pp20) REVERT: G 68 ASN cc_start: 0.9527 (m-40) cc_final: 0.9131 (m110) REVERT: A 50 GLU cc_start: 0.9484 (mt-10) cc_final: 0.9038 (mt-10) REVERT: A 53 ARG cc_start: 0.9498 (ptm-80) cc_final: 0.9256 (ptm160) REVERT: A 54 TYR cc_start: 0.9425 (m-80) cc_final: 0.8976 (m-80) REVERT: A 59 GLU cc_start: 0.8717 (pm20) cc_final: 0.8379 (pm20) REVERT: A 60 LEU cc_start: 0.9052 (mm) cc_final: 0.8803 (mm) REVERT: A 87 SER cc_start: 0.8902 (p) cc_final: 0.8442 (t) REVERT: A 90 MET cc_start: 0.9071 (mpp) cc_final: 0.8695 (mmm) REVERT: A 94 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8159 (mt-10) REVERT: A 120 MET cc_start: 0.8334 (mmt) cc_final: 0.7662 (mmm) REVERT: A 130 ILE cc_start: 0.9413 (mm) cc_final: 0.9062 (mm) REVERT: B 31 LYS cc_start: 0.9455 (tmtt) cc_final: 0.9193 (tmtt) REVERT: B 49 LEU cc_start: 0.9490 (mm) cc_final: 0.9077 (tp) REVERT: B 63 GLU cc_start: 0.8815 (pp20) cc_final: 0.8533 (pp20) REVERT: B 68 ASP cc_start: 0.8869 (m-30) cc_final: 0.8633 (m-30) REVERT: C 36 LYS cc_start: 0.9290 (mmtm) cc_final: 0.9043 (mtmt) REVERT: C 84 GLN cc_start: 0.9158 (tp-100) cc_final: 0.8862 (tp-100) REVERT: C 90 ASP cc_start: 0.8470 (t0) cc_final: 0.8154 (t0) REVERT: D 34 LYS cc_start: 0.8728 (pptt) cc_final: 0.8424 (mmtp) REVERT: D 76 GLU cc_start: 0.9282 (mm-30) cc_final: 0.8991 (mm-30) REVERT: E 50 GLU cc_start: 0.8770 (tp30) cc_final: 0.8146 (tp30) REVERT: E 73 GLU cc_start: 0.9199 (pt0) cc_final: 0.8667 (pt0) REVERT: E 77 ASP cc_start: 0.9443 (m-30) cc_final: 0.9204 (m-30) REVERT: E 119 ILE cc_start: 0.9488 (pt) cc_final: 0.9282 (pt) REVERT: E 120 MET cc_start: 0.8920 (mmm) cc_final: 0.8323 (mmm) REVERT: F 49 LEU cc_start: 0.9425 (mt) cc_final: 0.9048 (mt) REVERT: F 63 GLU cc_start: 0.9318 (pt0) cc_final: 0.8918 (pp20) REVERT: F 64 ASN cc_start: 0.9598 (t0) cc_final: 0.9291 (t0) REVERT: F 74 GLU cc_start: 0.9225 (tm-30) cc_final: 0.9002 (tm-30) REVERT: F 84 MET cc_start: 0.9224 (tpt) cc_final: 0.8952 (tpp) REVERT: H 42 TYR cc_start: 0.7231 (t80) cc_final: 0.6065 (t80) REVERT: H 59 MET cc_start: 0.9031 (tpp) cc_final: 0.8751 (tpt) REVERT: H 69 ILE cc_start: 0.8945 (mm) cc_final: 0.8540 (mm) REVERT: H 109 HIS cc_start: 0.8936 (m-70) cc_final: 0.8032 (m-70) REVERT: H 113 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8525 (mm-30) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.2853 time to fit residues: 122.7209 Evaluate side-chains 243 residues out of total 835 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 31 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 10.0000 chunk 104 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 HIS ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.069546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.049575 restraints weight = 90235.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.050497 restraints weight = 50312.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051171 restraints weight = 35319.629| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.6528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 15895 Z= 0.460 Angle : 0.837 12.568 22928 Z= 0.479 Chirality : 0.045 0.242 2563 Planarity : 0.007 0.097 1719 Dihedral : 31.000 155.304 4918 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 24.59 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.46 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % 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: 0.35 (0.26), residues: 964 helix: 0.92 (0.20), residues: 628 sheet: -1.94 (1.01), residues: 24 loop : -0.88 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP P 244 HIS 0.008 0.002 HIS G 124 PHE 0.015 0.002 PHE D 65 TYR 0.033 0.003 TYR B 88 ARG 0.008 0.001 ARG O 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3071.23 seconds wall clock time: 58 minutes 20.66 seconds (3500.66 seconds total)