Starting phenix.real_space_refine on Wed Aug 5 22:00:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k44_62044/08_2026/9k44_62044.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k44_62044/08_2026/9k44_62044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k44_62044/08_2026/9k44_62044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k44_62044/08_2026/9k44_62044.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k44_62044/08_2026/9k44_62044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k44_62044/08_2026/9k44_62044.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.038 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 289 5.49 5 S 12 5.16 5 C 6587 2.51 5 N 2172 2.21 5 O 2780 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11840 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 783 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 89} Chain: "I" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2950 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2992 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.39, per 1000 atoms: 0.20 Number of scatterers: 11840 At special positions: 0 Unit cell: (124.3, 95.7, 116.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 289 15.00 O 2780 8.00 N 2172 7.00 C 6587 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: 0.94 Conformation dependent library (CDL) restraints added in 229.0 milliseconds 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1396 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 72.9% alpha, 2.7% beta 144 base pairs and 253 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.767A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 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: 3.603A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.621A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 38 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 91 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'D' and resid 60 through 72 Processing helix chain 'D' and resid 78 through 107 Processing helix chain 'D' and resid 113 through 125 Processing helix chain 'D' and resid 126 through 147 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.824A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER E 57 " --> pdb=" O LYS E 53 " (cutoff:3.500A) 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 removed outlier: 3.731A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.678A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.673A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 Processing helix chain 'G' and resid 27 through 38 Processing helix chain 'G' and resid 47 through 74 Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 removed outlier: 3.512A pdb=" N ASN H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 146 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.133A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.358A pdb=" N ARG C 43 " --> pdb=" O ILE D 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.969A pdb=" N THR C 102 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.032A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.437A pdb=" N ARG G 43 " --> pdb=" O ILE H 112 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 403 hydrogen bonds defined for protein. 1197 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 694 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 253 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.20 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: 2030 1.33 - 1.45: 4175 1.45 - 1.57: 5843 1.57 - 1.68: 577 1.68 - 1.80: 22 Bond restraints: 12647 Sorted by residual: bond pdb=" O3' DG I -26 " pdb=" P DT I -25 " ideal model delta sigma weight residual 1.607 1.666 -0.059 1.20e-02 6.94e+03 2.39e+01 bond pdb=" O3' DT J -36 " pdb=" P DG J -35 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.20e-02 6.94e+03 1.91e+01 bond pdb=" O3' DC I 47 " pdb=" P DC I 48 " ideal model delta sigma weight residual 1.607 1.653 -0.046 1.20e-02 6.94e+03 1.44e+01 bond pdb=" O3' DA I -47 " pdb=" P DT I -46 " ideal model delta sigma weight residual 1.607 1.650 -0.043 1.20e-02 6.94e+03 1.28e+01 bond pdb=" C3' DC I -18 " pdb=" C2' DC I -18 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 ... (remaining 12642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 17089 1.52 - 3.03: 1182 3.03 - 4.55: 49 4.55 - 6.07: 7 6.07 - 7.58: 2 Bond angle restraints: 18329 Sorted by residual: angle pdb=" N GLN C 25 " pdb=" CA GLN C 25 " pdb=" C GLN C 25 " ideal model delta sigma weight residual 114.12 107.53 6.59 1.39e+00 5.18e-01 2.25e+01 angle pdb=" N3 DT I -11 " pdb=" C4 DT I -11 " pdb=" O4 DT I -11 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J 8 " pdb=" C4 DT J 8 " pdb=" O4 DT J 8 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT I -33 " pdb=" C4 DT I -33 " pdb=" O4 DT I -33 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I 8 " pdb=" C4 DT I 8 " pdb=" O4 DT I 8 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 18324 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4244 17.63 - 35.27: 1175 35.27 - 52.90: 1148 52.90 - 70.53: 344 70.53 - 88.16: 28 Dihedral angle restraints: 6939 sinusoidal: 4779 harmonic: 2160 Sorted by residual: dihedral pdb=" CG ARG A 128 " pdb=" CD ARG A 128 " pdb=" NE ARG A 128 " pdb=" CZ ARG A 128 " ideal model delta sinusoidal sigma weight residual -180.00 -135.67 -44.33 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CA PRO H 126 " pdb=" C PRO H 126 " pdb=" N GLY H 127 " pdb=" CA GLY H 127 " ideal model delta harmonic sigma weight residual 180.00 163.87 16.13 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA PRO D 126 " pdb=" C PRO D 126 " pdb=" N GLY D 127 " pdb=" CA GLY D 127 " ideal model delta harmonic sigma weight residual 180.00 163.96 16.04 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 6936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1306 0.036 - 0.072: 552 0.072 - 0.108: 195 0.108 - 0.143: 35 0.143 - 0.179: 3 Chirality restraints: 2091 Sorted by residual: chirality pdb=" CA PHE C 26 " pdb=" N PHE C 26 " pdb=" C PHE C 26 " pdb=" CB PHE C 26 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.04e-01 chirality pdb=" C3' DT I 45 " pdb=" C4' DT I 45 " pdb=" O3' DT I 45 " pdb=" C2' DT I 45 " both_signs ideal model delta sigma weight residual False -2.73 -2.91 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" P DC I -49 " pdb=" OP1 DC I -49 " pdb=" OP2 DC I -49 " pdb=" O5' DC I -49 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.14 2.00e-01 2.50e+01 5.24e-01 ... (remaining 2088 not shown) Planarity restraints: 1312 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 69 " -0.020 2.00e-02 2.50e+03 8.87e-03 2.17e+00 pdb=" N9 DA I 69 " 0.019 2.00e-02 2.50e+03 pdb=" C8 DA I 69 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 69 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 69 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 69 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 69 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 69 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I 69 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DA I 69 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DA I 69 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 125 " 0.024 5.00e-02 4.00e+02 3.66e-02 2.14e+00 pdb=" N PRO H 126 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -58 " 0.017 2.00e-02 2.50e+03 8.15e-03 1.83e+00 pdb=" N9 DA I -58 " -0.020 2.00e-02 2.50e+03 pdb=" C8 DA I -58 " -0.001 2.00e-02 2.50e+03 pdb=" N7 DA I -58 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -58 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -58 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -58 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DA I -58 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -58 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -58 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -58 " -0.001 2.00e-02 2.50e+03 ... (remaining 1309 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1230 2.74 - 3.28: 10389 3.28 - 3.82: 23052 3.82 - 4.36: 26952 4.36 - 4.90: 39169 Nonbonded interactions: 100792 Sorted by model distance: nonbonded pdb=" O ASP G 91 " pdb=" OG SER G 95 " model vdw 2.206 3.040 nonbonded pdb=" O ASP C 91 " pdb=" OG SER C 95 " model vdw 2.222 3.040 nonbonded pdb=" NH2 ARG G 30 " pdb=" OH TYR H 63 " model vdw 2.263 3.120 nonbonded pdb=" N GLU C 93 " pdb=" OE1 GLU C 93 " model vdw 2.279 3.120 nonbonded pdb=" N GLU A 59 " pdb=" OE1 GLU A 59 " model vdw 2.280 3.120 ... (remaining 100787 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' } ncs_group { reference = chain 'D' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.800 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 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 : 0.006 0.059 12647 Z= 0.507 Angle : 0.742 7.583 18329 Z= 0.675 Chirality : 0.044 0.179 2091 Planarity : 0.004 0.037 1312 Dihedral : 28.802 88.162 5543 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.16 % Allowed : 14.68 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.31), residues: 730 helix: 2.85 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -0.48 (0.39), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 72 TYR 0.013 0.001 TYR B 98 PHE 0.010 0.001 PHE C 26 HIS 0.001 0.001 HIS E 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00574 / 0.51 (12647) covalent geometry : angle 0.74211 / 0.68 (18329) hydrogen bonds : bond 0.11223 / 7.96 ( 750) hydrogen bonds : angle 4.34034 / 3.14 ( 1891) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 98 GLN cc_start: 0.7888 (mm-40) cc_final: 0.6472 (mm-40) outliers start: 1 outliers final: 1 residues processed: 227 average time/residue: 0.0962 time to fit residues: 30.3245 Evaluate side-chains 190 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 189 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 96 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 75 HIS D 70 GLN E 39 HIS F 75 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.063485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.044268 restraints weight = 59671.640| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.62 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12647 Z= 0.149 Angle : 0.652 7.889 18329 Z= 0.383 Chirality : 0.044 0.270 2091 Planarity : 0.004 0.032 1312 Dihedral : 31.534 88.501 4074 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.74 % Allowed : 16.77 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.31), residues: 730 helix: 2.70 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.28 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 72 TYR 0.017 0.002 TYR F 88 PHE 0.018 0.001 PHE H 93 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.15 (12647) covalent geometry : angle 0.65202 / 0.38 (18329) hydrogen bonds : bond 0.05274 / 3.63 ( 750) hydrogen bonds : angle 3.09295 / 2.28 ( 1891) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 204 time to evaluate : 0.198 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: C 91 ASP cc_start: 0.7915 (t70) cc_final: 0.7498 (t70) REVERT: D 87 SER cc_start: 0.9567 (m) cc_final: 0.9296 (p) REVERT: D 91 ASP cc_start: 0.8598 (t0) cc_final: 0.8381 (t0) REVERT: F 84 MET cc_start: 0.8684 (mmm) cc_final: 0.8342 (mmm) REVERT: F 88 TYR cc_start: 0.9132 (m-80) cc_final: 0.8005 (m-80) REVERT: G 72 ARG cc_start: 0.9197 (ttm-80) cc_final: 0.8977 (ttp80) REVERT: G 89 ARG cc_start: 0.8811 (tpp80) cc_final: 0.8526 (tpp80) REVERT: G 91 ASP cc_start: 0.7805 (t70) cc_final: 0.7516 (t0) REVERT: H 94 GLU cc_start: 0.8834 (tp30) cc_final: 0.8212 (tp30) REVERT: H 98 GLN cc_start: 0.8899 (mm-40) cc_final: 0.8250 (mm-40) REVERT: H 99 GLU cc_start: 0.8978 (tp30) cc_final: 0.8749 (tp30) outliers start: 17 outliers final: 8 residues processed: 208 average time/residue: 0.0935 time to fit residues: 27.5649 Evaluate side-chains 202 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 194 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 84 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 101 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 88 optimal weight: 30.0000 chunk 29 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 18 optimal weight: 0.0040 chunk 85 optimal weight: 50.0000 chunk 28 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 36 optimal weight: 10.0000 overall best weight: 1.1196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN E 76 GLN G 74 ASN H 70 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.062622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.045458 restraints weight = 63290.310| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.55 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 12647 Z= 0.140 Angle : 0.609 7.114 18329 Z= 0.363 Chirality : 0.042 0.225 2091 Planarity : 0.004 0.034 1312 Dihedral : 31.530 88.531 4074 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.94 % Allowed : 18.55 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.31), residues: 730 helix: 2.85 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.21 (0.43), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 30 TYR 0.026 0.002 TYR B 88 PHE 0.016 0.001 PHE D 93 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (12647) covalent geometry : angle 0.60891 / 0.36 (18329) hydrogen bonds : bond 0.04797 / 3.31 ( 750) hydrogen bonds : angle 2.92503 / 2.16 ( 1891) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 201 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 84 MET cc_start: 0.8737 (mmp) cc_final: 0.8266 (mmm) REVERT: B 88 TYR cc_start: 0.9007 (m-80) cc_final: 0.8632 (m-80) REVERT: C 91 ASP cc_start: 0.7683 (t70) cc_final: 0.7335 (t0) REVERT: C 109 MET cc_start: 0.7083 (mpp) cc_final: 0.6792 (mtm) REVERT: D 87 SER cc_start: 0.9552 (m) cc_final: 0.9283 (p) REVERT: D 91 ASP cc_start: 0.8780 (t0) cc_final: 0.8523 (t0) REVERT: D 94 GLU cc_start: 0.8800 (tp30) cc_final: 0.8245 (tp30) REVERT: D 98 GLN cc_start: 0.8969 (mm110) cc_final: 0.8593 (mm110) REVERT: F 84 MET cc_start: 0.8445 (mmm) cc_final: 0.8121 (mmt) REVERT: F 88 TYR cc_start: 0.9193 (m-80) cc_final: 0.8855 (m-80) REVERT: G 89 ARG cc_start: 0.8847 (tpp80) cc_final: 0.8327 (tpp80) REVERT: G 91 ASP cc_start: 0.8096 (t70) cc_final: 0.7750 (t0) REVERT: H 94 GLU cc_start: 0.8890 (tp30) cc_final: 0.8510 (tp30) REVERT: H 98 GLN cc_start: 0.8944 (mm-40) cc_final: 0.8434 (mm110) REVERT: H 99 GLU cc_start: 0.8939 (tp30) cc_final: 0.8503 (tp30) outliers start: 12 outliers final: 9 residues processed: 204 average time/residue: 0.0883 time to fit residues: 25.6339 Evaluate side-chains 198 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 73 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 83 optimal weight: 20.0000 chunk 21 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.6327 > 50:) chunk 62 optimal weight: 8.9990 chunk 86 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 93 optimal weight: 20.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 70 GLN D 98 GLN G 74 ASN H 70 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.060030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.041347 restraints weight = 61317.395| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.59 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12647 Z= 0.250 Angle : 0.714 11.120 18329 Z= 0.400 Chirality : 0.046 0.218 2091 Planarity : 0.004 0.036 1312 Dihedral : 31.852 88.967 4074 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.39 % Allowed : 18.06 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.32), residues: 730 helix: 2.83 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.36 (0.45), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 72 TYR 0.014 0.002 TYR B 88 PHE 0.010 0.002 PHE A 84 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.25 (12647) covalent geometry : angle 0.71415 / 0.40 (18329) hydrogen bonds : bond 0.07454 / 5.22 ( 750) hydrogen bonds : angle 3.35173 / 2.48 ( 1891) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9388 (mtmt) cc_final: 0.9158 (mtmm) REVERT: B 53 GLU cc_start: 0.9018 (tp30) cc_final: 0.8728 (tp30) REVERT: B 84 MET cc_start: 0.8730 (mmp) cc_final: 0.8255 (mmm) REVERT: C 91 ASP cc_start: 0.7896 (t70) cc_final: 0.7546 (t0) REVERT: C 109 MET cc_start: 0.7596 (mpp) cc_final: 0.7253 (mtm) REVERT: D 91 ASP cc_start: 0.8805 (t0) cc_final: 0.8580 (t0) REVERT: D 94 GLU cc_start: 0.8769 (tp30) cc_final: 0.8399 (tp30) REVERT: D 98 GLN cc_start: 0.8966 (mm-40) cc_final: 0.8635 (mm110) REVERT: F 84 MET cc_start: 0.8617 (mmm) cc_final: 0.7812 (mmm) REVERT: G 72 ARG cc_start: 0.9195 (ttm-80) cc_final: 0.8900 (ttp80) REVERT: G 91 ASP cc_start: 0.8058 (t70) cc_final: 0.7490 (t70) REVERT: G 93 GLU cc_start: 0.9177 (pm20) cc_final: 0.8953 (pm20) REVERT: H 94 GLU cc_start: 0.8917 (tp30) cc_final: 0.8299 (tp30) REVERT: H 98 GLN cc_start: 0.9064 (mm-40) cc_final: 0.8457 (mm110) REVERT: H 116 GLU cc_start: 0.8782 (mp0) cc_final: 0.8245 (mp0) outliers start: 21 outliers final: 15 residues processed: 190 average time/residue: 0.0917 time to fit residues: 24.5684 Evaluate side-chains 189 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 174 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 77 THR Chi-restraints excluded: chain H residue 87 SER Chi-restraints excluded: chain H residue 89 ILE Chi-restraints excluded: chain H residue 121 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN D 70 GLN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.061296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.042383 restraints weight = 62492.820| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.67 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12647 Z= 0.136 Angle : 0.617 10.829 18329 Z= 0.360 Chirality : 0.042 0.209 2091 Planarity : 0.004 0.032 1312 Dihedral : 31.730 86.992 4074 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 2.90 % Allowed : 18.71 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.32), residues: 730 helix: 2.93 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.27 (0.44), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 89 TYR 0.028 0.002 TYR B 88 PHE 0.008 0.001 PHE D 93 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.14 (12647) covalent geometry : angle 0.61668 / 0.36 (18329) hydrogen bonds : bond 0.04538 / 3.14 ( 750) hydrogen bonds : angle 2.94732 / 2.18 ( 1891) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 196 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8957 (tp30) cc_final: 0.8694 (tp30) REVERT: B 84 MET cc_start: 0.8667 (mmp) cc_final: 0.8439 (mmm) REVERT: B 85 ASP cc_start: 0.9348 (m-30) cc_final: 0.9081 (m-30) REVERT: C 91 ASP cc_start: 0.7754 (t70) cc_final: 0.7338 (t0) REVERT: C 109 MET cc_start: 0.7413 (mpp) cc_final: 0.7096 (mtm) REVERT: D 91 ASP cc_start: 0.8785 (t0) cc_final: 0.8545 (t0) REVERT: D 94 GLU cc_start: 0.8870 (tp30) cc_final: 0.8459 (tp30) REVERT: D 98 GLN cc_start: 0.9082 (mm-40) cc_final: 0.8701 (mm110) REVERT: E 76 GLN cc_start: 0.9121 (tt0) cc_final: 0.8853 (tm-30) REVERT: F 84 MET cc_start: 0.8597 (mmm) cc_final: 0.8349 (mmm) REVERT: F 88 TYR cc_start: 0.9179 (m-80) cc_final: 0.8865 (m-80) REVERT: G 72 ARG cc_start: 0.9214 (ttm-80) cc_final: 0.8908 (ttp80) REVERT: G 91 ASP cc_start: 0.7991 (t70) cc_final: 0.7620 (t0) REVERT: H 94 GLU cc_start: 0.8941 (tp30) cc_final: 0.8178 (tp30) REVERT: H 98 GLN cc_start: 0.9074 (mm-40) cc_final: 0.8362 (mm110) REVERT: H 116 GLU cc_start: 0.8872 (mp0) cc_final: 0.8353 (mp0) outliers start: 18 outliers final: 14 residues processed: 200 average time/residue: 0.0887 time to fit residues: 25.0400 Evaluate side-chains 203 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 74 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 82 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 90 ASN D 107 ASN E 113 HIS G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.061360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.042442 restraints weight = 61238.273| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.63 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 12647 Z= 0.134 Angle : 0.622 11.344 18329 Z= 0.362 Chirality : 0.041 0.203 2091 Planarity : 0.004 0.034 1312 Dihedral : 31.604 86.332 4074 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.90 % Allowed : 20.48 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.31), residues: 730 helix: 2.93 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.22 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 30 TYR 0.027 0.002 TYR B 88 PHE 0.008 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.13 (12647) covalent geometry : angle 0.62193 / 0.36 (18329) hydrogen bonds : bond 0.04460 / 3.10 ( 750) hydrogen bonds : angle 2.89951 / 2.14 ( 1891) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9203 (tt0) cc_final: 0.8779 (tm-30) REVERT: B 53 GLU cc_start: 0.8918 (tp30) cc_final: 0.8650 (tp30) REVERT: B 85 ASP cc_start: 0.9349 (m-30) cc_final: 0.9070 (m-30) REVERT: C 91 ASP cc_start: 0.7830 (t70) cc_final: 0.7432 (t0) REVERT: D 91 ASP cc_start: 0.8814 (t0) cc_final: 0.8565 (t0) REVERT: D 94 GLU cc_start: 0.8874 (tp30) cc_final: 0.8328 (tp30) REVERT: D 98 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8586 (mm110) REVERT: D 116 GLU cc_start: 0.8331 (mp0) cc_final: 0.8054 (mp0) REVERT: E 76 GLN cc_start: 0.9115 (tt0) cc_final: 0.8843 (tm-30) REVERT: F 84 MET cc_start: 0.8612 (mmm) cc_final: 0.8339 (mmm) REVERT: F 88 TYR cc_start: 0.9179 (m-80) cc_final: 0.8874 (m-80) REVERT: G 91 ASP cc_start: 0.7957 (t70) cc_final: 0.7562 (t0) REVERT: H 94 GLU cc_start: 0.8912 (tp30) cc_final: 0.8248 (tp30) REVERT: H 98 GLN cc_start: 0.9130 (mm-40) cc_final: 0.8571 (mm110) REVERT: H 116 GLU cc_start: 0.8888 (mp0) cc_final: 0.8661 (mp0) outliers start: 18 outliers final: 10 residues processed: 197 average time/residue: 0.0878 time to fit residues: 24.6398 Evaluate side-chains 197 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 187 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 99 GLU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 73 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 94 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 0.0050 chunk 24 optimal weight: 2.9990 overall best weight: 1.2998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.060663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.043453 restraints weight = 63927.366| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.55 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12647 Z= 0.141 Angle : 0.630 11.438 18329 Z= 0.364 Chirality : 0.041 0.203 2091 Planarity : 0.004 0.033 1312 Dihedral : 31.578 85.682 4073 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.26 % Allowed : 21.61 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.36 (0.31), residues: 730 helix: 2.97 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.19 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 72 TYR 0.030 0.002 TYR B 88 PHE 0.007 0.001 PHE A 67 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.14 (12647) covalent geometry : angle 0.63007 / 0.36 (18329) hydrogen bonds : bond 0.04473 / 3.11 ( 750) hydrogen bonds : angle 2.90138 / 2.14 ( 1891) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 189 time to evaluate : 0.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.9206 (tt0) cc_final: 0.8772 (tm-30) REVERT: B 53 GLU cc_start: 0.8927 (tp30) cc_final: 0.8670 (tp30) REVERT: C 36 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8898 (mmmm) REVERT: C 91 ASP cc_start: 0.7801 (t70) cc_final: 0.7434 (t0) REVERT: C 109 MET cc_start: 0.7062 (mpp) cc_final: 0.6843 (mtm) REVERT: D 91 ASP cc_start: 0.8834 (t0) cc_final: 0.8571 (t0) REVERT: D 94 GLU cc_start: 0.8879 (tp30) cc_final: 0.8278 (tp30) REVERT: D 98 GLN cc_start: 0.9149 (mm-40) cc_final: 0.8543 (mm110) REVERT: D 116 GLU cc_start: 0.8450 (mp0) cc_final: 0.8142 (mp0) REVERT: E 76 GLN cc_start: 0.9100 (tt0) cc_final: 0.8811 (tm-30) REVERT: F 84 MET cc_start: 0.8658 (mmm) cc_final: 0.8346 (mmm) REVERT: F 88 TYR cc_start: 0.9197 (m-80) cc_final: 0.8898 (m-80) REVERT: G 91 ASP cc_start: 0.8031 (t70) cc_final: 0.7682 (t0) REVERT: G 108 VAL cc_start: 0.8807 (m) cc_final: 0.8563 (p) REVERT: G 109 MET cc_start: 0.6833 (mpp) cc_final: 0.6409 (mtp) REVERT: H 94 GLU cc_start: 0.8899 (tp30) cc_final: 0.8373 (tp30) REVERT: H 98 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8622 (mm110) REVERT: H 116 GLU cc_start: 0.8937 (mp0) cc_final: 0.8646 (mp0) outliers start: 14 outliers final: 9 residues processed: 193 average time/residue: 0.0961 time to fit residues: 26.4044 Evaluate side-chains 191 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 146 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 83 optimal weight: 20.0000 chunk 37 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.061100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.042297 restraints weight = 61310.662| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.66 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 12647 Z= 0.139 Angle : 0.639 11.911 18329 Z= 0.368 Chirality : 0.042 0.228 2091 Planarity : 0.004 0.033 1312 Dihedral : 31.528 84.806 4073 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.10 % Allowed : 22.26 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.31), residues: 730 helix: 2.93 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.15 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 30 TYR 0.028 0.002 TYR B 88 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (12647) covalent geometry : angle 0.63862 / 0.37 (18329) hydrogen bonds : bond 0.04328 / 3.01 ( 750) hydrogen bonds : angle 2.96113 / 2.19 ( 1891) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.297 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: A 76 GLN cc_start: 0.9174 (tt0) cc_final: 0.8785 (tm-30) REVERT: B 53 GLU cc_start: 0.8875 (tp30) cc_final: 0.8672 (tp30) REVERT: C 36 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8925 (mmmm) REVERT: C 91 ASP cc_start: 0.7891 (t70) cc_final: 0.7508 (t0) REVERT: C 109 MET cc_start: 0.7171 (mpp) cc_final: 0.6898 (mtm) REVERT: D 91 ASP cc_start: 0.8793 (t0) cc_final: 0.8548 (t0) REVERT: D 94 GLU cc_start: 0.8823 (tp30) cc_final: 0.8208 (tp30) REVERT: D 98 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8466 (mm110) REVERT: D 116 GLU cc_start: 0.8424 (mp0) cc_final: 0.8170 (mp0) REVERT: E 76 GLN cc_start: 0.9044 (tt0) cc_final: 0.8790 (tm-30) REVERT: F 74 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8313 (mm-30) REVERT: F 84 MET cc_start: 0.8599 (mmm) cc_final: 0.8354 (mmm) REVERT: F 88 TYR cc_start: 0.9166 (m-80) cc_final: 0.8857 (m-80) REVERT: G 91 ASP cc_start: 0.8089 (t70) cc_final: 0.7734 (t0) REVERT: G 108 VAL cc_start: 0.8812 (m) cc_final: 0.8602 (p) REVERT: G 109 MET cc_start: 0.6847 (mpp) cc_final: 0.6451 (mtp) REVERT: H 94 GLU cc_start: 0.8808 (tp30) cc_final: 0.8282 (tp30) REVERT: H 98 GLN cc_start: 0.9113 (mm-40) cc_final: 0.8612 (mm110) REVERT: H 116 GLU cc_start: 0.8862 (mp0) cc_final: 0.8582 (mp0) outliers start: 13 outliers final: 12 residues processed: 196 average time/residue: 0.0868 time to fit residues: 24.2476 Evaluate side-chains 197 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 185 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 74 ASN Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 146 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 59 optimal weight: 0.0670 chunk 29 optimal weight: 8.9990 chunk 91 optimal weight: 20.0000 chunk 4 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.8124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.061533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.042761 restraints weight = 61088.602| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 2.67 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 12647 Z= 0.137 Angle : 0.639 12.324 18329 Z= 0.368 Chirality : 0.042 0.201 2091 Planarity : 0.004 0.033 1312 Dihedral : 31.485 84.267 4073 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.45 % Allowed : 22.42 % Favored : 76.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.31), residues: 730 helix: 2.87 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.12 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 30 TYR 0.025 0.002 TYR B 88 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.14 (12647) covalent geometry : angle 0.63885 / 0.37 (18329) hydrogen bonds : bond 0.04232 / 2.95 ( 750) hydrogen bonds : angle 2.90119 / 2.13 ( 1891) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 188 time to evaluate : 0.198 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: A 76 GLN cc_start: 0.9187 (tt0) cc_final: 0.8770 (tm-30) REVERT: B 53 GLU cc_start: 0.8880 (tp30) cc_final: 0.8665 (tp30) REVERT: C 91 ASP cc_start: 0.7785 (t70) cc_final: 0.7460 (t0) REVERT: C 109 MET cc_start: 0.7154 (mpp) cc_final: 0.6912 (mtm) REVERT: D 91 ASP cc_start: 0.8836 (t0) cc_final: 0.8582 (t0) REVERT: D 94 GLU cc_start: 0.8863 (tp30) cc_final: 0.8241 (tp30) REVERT: D 98 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8462 (mm110) REVERT: D 116 GLU cc_start: 0.8475 (mp0) cc_final: 0.8163 (mp0) REVERT: E 76 GLN cc_start: 0.9065 (tt0) cc_final: 0.8765 (tm-30) REVERT: F 84 MET cc_start: 0.8675 (mmm) cc_final: 0.8443 (mmm) REVERT: F 88 TYR cc_start: 0.9194 (m-80) cc_final: 0.8897 (m-80) REVERT: G 91 ASP cc_start: 0.7979 (t70) cc_final: 0.7646 (t0) REVERT: G 108 VAL cc_start: 0.8805 (m) cc_final: 0.8583 (p) REVERT: G 109 MET cc_start: 0.6772 (mpp) cc_final: 0.6399 (mtp) REVERT: H 94 GLU cc_start: 0.8836 (tp30) cc_final: 0.8326 (tp30) REVERT: H 98 GLN cc_start: 0.9134 (mm-40) cc_final: 0.8570 (mm110) REVERT: H 116 GLU cc_start: 0.8904 (mp0) cc_final: 0.8592 (mp0) outliers start: 9 outliers final: 7 residues processed: 191 average time/residue: 0.0906 time to fit residues: 24.3836 Evaluate side-chains 191 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 184 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain F residue 97 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 9 optimal weight: 0.0870 chunk 76 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 3 optimal weight: 3.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.059429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.040580 restraints weight = 61605.435| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.57 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12647 Z= 0.243 Angle : 0.744 11.940 18329 Z= 0.410 Chirality : 0.045 0.226 2091 Planarity : 0.004 0.035 1312 Dihedral : 31.844 86.214 4073 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.61 % Allowed : 22.74 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.94 (0.31), residues: 730 helix: 2.63 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.34 (0.45), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 72 TYR 0.029 0.002 TYR B 88 PHE 0.011 0.002 PHE G 26 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.24 (12647) covalent geometry : angle 0.74375 / 0.41 (18329) hydrogen bonds : bond 0.07590 / 5.33 ( 750) hydrogen bonds : angle 3.30326 / 2.44 ( 1891) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1460 Ramachandran restraints generated. 730 Oldfield, 0 Emsley, 730 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 0.249 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: A 76 GLN cc_start: 0.9182 (tt0) cc_final: 0.8759 (tm-30) REVERT: B 53 GLU cc_start: 0.9004 (tp30) cc_final: 0.8794 (tp30) REVERT: C 91 ASP cc_start: 0.7899 (t70) cc_final: 0.7529 (t0) REVERT: D 91 ASP cc_start: 0.8843 (t0) cc_final: 0.8577 (t0) REVERT: D 94 GLU cc_start: 0.8813 (tp30) cc_final: 0.8100 (tp30) REVERT: D 98 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8377 (mm110) REVERT: E 76 GLN cc_start: 0.9074 (tt0) cc_final: 0.8808 (tm-30) REVERT: F 53 GLU cc_start: 0.9021 (tp30) cc_final: 0.8735 (tp30) REVERT: G 91 ASP cc_start: 0.7971 (t70) cc_final: 0.7428 (t0) REVERT: G 93 GLU cc_start: 0.9059 (pm20) cc_final: 0.8845 (pm20) REVERT: H 94 GLU cc_start: 0.8812 (tp30) cc_final: 0.8241 (tp30) REVERT: H 98 GLN cc_start: 0.9147 (mm-40) cc_final: 0.8547 (mm110) REVERT: H 116 GLU cc_start: 0.8948 (mp0) cc_final: 0.8693 (mp0) outliers start: 10 outliers final: 8 residues processed: 171 average time/residue: 0.0939 time to fit residues: 22.7464 Evaluate side-chains 168 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 160 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 57 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 53 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 88 optimal weight: 30.0000 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 81 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 18 optimal weight: 0.2980 chunk 19 optimal weight: 3.9990 chunk 97 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN D 107 ASN G 74 ASN G 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.059895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040923 restraints weight = 62443.963| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.69 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12647 Z= 0.150 Angle : 0.665 12.523 18329 Z= 0.379 Chirality : 0.043 0.216 2091 Planarity : 0.004 0.032 1312 Dihedral : 31.733 84.867 4073 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.13 % Allowed : 23.06 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.31), residues: 730 helix: 2.80 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.32 (0.44), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 72 TYR 0.028 0.002 TYR B 88 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (12647) covalent geometry : angle 0.66516 / 0.38 (18329) hydrogen bonds : bond 0.04691 / 3.28 ( 750) hydrogen bonds : angle 3.04223 / 2.24 ( 1891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1751.03 seconds wall clock time: 30 minutes 40.64 seconds (1840.64 seconds total)