Starting phenix.real_space_refine on Fri Jul 3 03:56:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k44_62044/07_2026/9k44_62044.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k44_62044/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9k44_62044/07_2026/9k44_62044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k44_62044/07_2026/9k44_62044.map" model { file = "/net/cci-nas-00/data/ceres_data/9k44_62044/07_2026/9k44_62044.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k44_62044/07_2026/9k44_62044.cif" } 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-dev-6108/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: 2.45, per 1000 atoms: 0.21 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: 0.77 Conformation dependent library (CDL) restraints added in 238.2 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: 1.84 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: 2.02 Time building geometry restraints manager: 1.17 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 1.50e-02 4.44e+03 1.53e+01 bond pdb=" O3' DT J -36 " pdb=" P DG J -35 " ideal model delta sigma weight residual 1.607 1.659 -0.052 1.50e-02 4.44e+03 1.22e+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 bond pdb=" C3' DG I -40 " pdb=" C2' DG I -40 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.10e+01 bond pdb=" C3' DA J -46 " pdb=" C2' DA J -46 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 12642 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 17105 1.52 - 3.03: 1167 3.03 - 4.55: 48 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: 1.310 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.880 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.800 ------------------------------------------------------------------------------- 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= 0.504 Angle : 0.734 7.583 18329 Z= 0.668 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 / 0.50 (12647) covalent geometry : angle 0.73436 / 0.67 (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 : 0.195 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: 0.1040 time to fit residues: 32.3135 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 : 0.217 ------------------------------------------------------------------------------- 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: 0.9980 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: 7.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 75 HIS E 39 HIS F 75 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.063484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.044253 restraints weight = 59216.458| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.60 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1225 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= 0.150 Angle : 0.637 7.616 18329 Z= 0.379 Chirality : 0.043 0.267 2091 Planarity : 0.004 0.031 1312 Dihedral : 31.611 88.524 4074 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.06 % Allowed : 16.77 % Favored : 80.16 % 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: 3.03 (0.31), residues: 730 helix: 2.73 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.29 (0.43), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 72 TYR 0.018 0.002 TYR B 51 PHE 0.015 0.001 PHE H 93 HIS 0.002 0.001 HIS A 87 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.15 (12647) covalent geometry : angle 0.63659 / 0.38 (18329) hydrogen bonds : bond 0.05271 / 3.63 ( 750) hydrogen bonds : angle 3.09785 / 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: 19 poor density : 202 time to evaluate : 0.232 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: 0.7907 (t70) cc_final: 0.7500 (t70) REVERT: D 87 SER cc_start: 0.9569 (m) cc_final: 0.9296 (p) REVERT: D 91 ASP cc_start: 0.8590 (t0) cc_final: 0.8379 (t0) REVERT: F 84 MET cc_start: 0.8687 (mmm) cc_final: 0.8346 (mmm) REVERT: F 88 TYR cc_start: 0.9129 (m-80) cc_final: 0.7968 (m-80) REVERT: G 72 ARG cc_start: 0.9199 (ttm-80) cc_final: 0.8979 (ttp80) REVERT: G 89 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8581 (tpp80) REVERT: G 91 ASP cc_start: 0.7802 (t70) cc_final: 0.7576 (t0) REVERT: H 94 GLU cc_start: 0.8827 (tp30) cc_final: 0.8227 (tp30) REVERT: H 98 GLN cc_start: 0.8891 (mm-40) cc_final: 0.8259 (mm-40) REVERT: H 99 GLU cc_start: 0.8981 (tp30) cc_final: 0.8754 (tp30) outliers start: 19 outliers final: 9 residues processed: 207 average time/residue: 0.1034 time to fit residues: 30.1333 Evaluate side-chains 201 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 191 time to evaluate : 0.184 ------------------------------------------------------------------------------- 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 84 ILE Chi-restraints excluded: chain C residue 88 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 89 ARG 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: 2.9990 chunk 10 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 chunk 85 optimal weight: 40.0000 chunk 28 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 chunk 52 optimal weight: 0.0470 chunk 6 optimal weight: 0.6980 chunk 36 optimal weight: 10.0000 overall best weight: 0.9058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 74 ASN D 70 GLN E 76 GLN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.062574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.045387 restraints weight = 63345.356| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.53 r_work: 0.2810 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1514 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= 0.137 Angle : 0.590 6.538 18329 Z= 0.357 Chirality : 0.042 0.225 2091 Planarity : 0.004 0.035 1312 Dihedral : 31.602 88.695 4074 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.10 % Allowed : 17.26 % Favored : 80.65 % 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: 3.23 (0.31), residues: 730 helix: 2.87 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.21 (0.43), residues: 184 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 0.013 0.001 PHE D 93 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (12647) covalent geometry : angle 0.58985 / 0.36 (18329) hydrogen bonds : bond 0.04673 / 3.22 ( 750) hydrogen bonds : angle 2.88755 / 2.13 ( 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 214 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 201 time to evaluate : 0.320 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: 0.9320 (mttm) cc_final: 0.9115 (mtmm) REVERT: B 84 MET cc_start: 0.9302 (mmp) cc_final: 0.8913 (mmm) REVERT: C 91 ASP cc_start: 0.7835 (t70) cc_final: 0.7450 (t0) REVERT: C 109 MET cc_start: 0.7240 (mpp) cc_final: 0.6918 (mtm) REVERT: D 87 SER cc_start: 0.9590 (m) cc_final: 0.9324 (p) REVERT: D 91 ASP cc_start: 0.9043 (t0) cc_final: 0.8801 (t0) REVERT: D 94 GLU cc_start: 0.9153 (tp30) cc_final: 0.8680 (tp30) REVERT: D 98 GLN cc_start: 0.9214 (mm110) cc_final: 0.8805 (mm110) REVERT: E 76 GLN cc_start: 0.9372 (tt0) cc_final: 0.9114 (tm-30) REVERT: F 84 MET cc_start: 0.9061 (mmm) cc_final: 0.8655 (mmt) REVERT: F 88 TYR cc_start: 0.9324 (m-80) cc_final: 0.8973 (m-80) REVERT: G 89 ARG cc_start: 0.8820 (tpp80) cc_final: 0.8348 (tpp80) REVERT: G 91 ASP cc_start: 0.8135 (t70) cc_final: 0.7777 (t0) REVERT: H 82 MET cc_start: 0.9208 (mmm) cc_final: 0.8982 (tpp) REVERT: H 94 GLU cc_start: 0.9283 (tp30) cc_final: 0.8971 (tp30) REVERT: H 98 GLN cc_start: 0.9316 (mm-40) cc_final: 0.8875 (mm110) REVERT: H 99 GLU cc_start: 0.9214 (tp30) cc_final: 0.8781 (tp30) outliers start: 13 outliers final: 9 residues processed: 206 average time/residue: 0.1004 time to fit residues: 29.2229 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 : 0.218 ------------------------------------------------------------------------------- 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 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 73 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 20.0000 chunk 21 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 86 optimal weight: 50.0000 chunk 75 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 93 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN G 74 ASN H 70 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.060693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.041586 restraints weight = 61375.679| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 2.67 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12647 Z= 0.224 Angle : 0.666 10.011 18329 Z= 0.383 Chirality : 0.044 0.206 2091 Planarity : 0.004 0.035 1312 Dihedral : 31.869 89.050 4074 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.26 % Allowed : 18.71 % Favored : 79.03 % 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: 3.22 (0.32), residues: 730 helix: 2.87 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.35 (0.44), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 89 TYR 0.030 0.002 TYR B 88 PHE 0.009 0.002 PHE A 84 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.22 (12647) covalent geometry : angle 0.66592 / 0.38 (18329) hydrogen bonds : bond 0.06858 / 4.80 ( 750) hydrogen bonds : angle 3.16198 / 2.35 ( 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 197 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 0.191 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: 0.9331 (mttm) cc_final: 0.9021 (mtmm) REVERT: B 84 MET cc_start: 0.8857 (mmp) cc_final: 0.8418 (mmm) REVERT: C 91 ASP cc_start: 0.7851 (t70) cc_final: 0.7443 (t0) REVERT: C 109 MET cc_start: 0.7525 (mpp) cc_final: 0.7195 (mtm) REVERT: D 87 SER cc_start: 0.9564 (m) cc_final: 0.9349 (p) REVERT: D 91 ASP cc_start: 0.8839 (t0) cc_final: 0.8612 (t0) REVERT: D 94 GLU cc_start: 0.8789 (tp30) cc_final: 0.8458 (tp30) REVERT: D 98 GLN cc_start: 0.8967 (mm-40) cc_final: 0.8634 (mm110) REVERT: F 84 MET cc_start: 0.8619 (mmm) cc_final: 0.7862 (mmm) REVERT: G 72 ARG cc_start: 0.9201 (ttm-80) cc_final: 0.8909 (ttp80) REVERT: G 91 ASP cc_start: 0.8026 (t70) cc_final: 0.7718 (t0) REVERT: H 94 GLU cc_start: 0.8913 (tp30) cc_final: 0.8314 (tp30) REVERT: H 98 GLN cc_start: 0.9063 (mm-40) cc_final: 0.8433 (mm110) REVERT: H 99 GLU cc_start: 0.8924 (tp30) cc_final: 0.8540 (tp30) outliers start: 14 outliers final: 8 residues processed: 188 average time/residue: 0.1019 time to fit residues: 26.8329 Evaluate side-chains 183 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.252 ------------------------------------------------------------------------------- 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 D residue 121 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR 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: 2.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.0670 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.6124 ------------------------------------------------------------------------------- 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 E 76 GLN G 74 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.061092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.042021 restraints weight = 62093.872| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 2.75 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12647 Z= 0.147 Angle : 0.614 12.062 18329 Z= 0.359 Chirality : 0.042 0.202 2091 Planarity : 0.004 0.033 1312 Dihedral : 31.830 87.909 4074 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.58 % Allowed : 19.35 % Favored : 78.06 % 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 (0.32), residues: 730 helix: 2.95 (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 0.004 0.000 ARG C 30 TYR 0.026 0.002 TYR B 88 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.15 (12647) covalent geometry : angle 0.61418 / 0.36 (18329) hydrogen bonds : bond 0.04694 / 3.26 ( 750) hydrogen bonds : angle 2.96227 / 2.19 ( 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 211 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 0.304 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 64 LYS cc_start: 0.9301 (mttm) cc_final: 0.8984 (mtmm) REVERT: B 53 GLU cc_start: 0.8925 (tp30) cc_final: 0.8663 (tp30) REVERT: B 85 ASP cc_start: 0.9311 (m-30) cc_final: 0.9047 (m-30) REVERT: C 91 ASP cc_start: 0.7891 (t70) cc_final: 0.7462 (t0) REVERT: D 87 SER cc_start: 0.9548 (m) cc_final: 0.9328 (p) REVERT: D 91 ASP cc_start: 0.8765 (t0) cc_final: 0.8531 (t0) REVERT: D 94 GLU cc_start: 0.8818 (tp30) cc_final: 0.8397 (tp30) REVERT: D 98 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8664 (mm110) REVERT: F 84 MET cc_start: 0.8558 (mmm) cc_final: 0.8313 (mmm) REVERT: F 88 TYR cc_start: 0.9120 (m-80) cc_final: 0.8821 (m-80) REVERT: G 72 ARG cc_start: 0.9196 (ttm-80) cc_final: 0.8907 (ttp80) REVERT: G 91 ASP cc_start: 0.8038 (t70) cc_final: 0.7647 (t0) REVERT: H 94 GLU cc_start: 0.8919 (tp30) cc_final: 0.8195 (tp30) REVERT: H 98 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8333 (mm110) REVERT: H 116 GLU cc_start: 0.8642 (mp0) cc_final: 0.8185 (mp0) outliers start: 16 outliers final: 11 residues processed: 199 average time/residue: 0.1117 time to fit residues: 31.3026 Evaluate side-chains 201 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 190 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 124 ILE 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 D residue 57 VAL Chi-restraints excluded: chain D residue 70 GLN Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 97 LEU 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: 0.7980 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 90 ASN E 76 GLN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.061294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.042633 restraints weight = 62536.774| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.65 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 12647 Z= 0.136 Angle : 0.613 11.640 18329 Z= 0.359 Chirality : 0.041 0.196 2091 Planarity : 0.004 0.038 1312 Dihedral : 31.706 86.978 4074 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.94 % Allowed : 20.48 % Favored : 77.58 % 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: 3.28 (0.31), residues: 730 helix: 2.91 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.24 (0.45), 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 0.008 0.001 PHE A 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (12647) covalent geometry : angle 0.61255 / 0.36 (18329) hydrogen bonds : bond 0.04444 / 3.08 ( 750) hydrogen bonds : angle 2.90873 / 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 209 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 197 time to evaluate : 0.321 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 64 LYS cc_start: 0.9316 (mttm) cc_final: 0.8980 (mtmm) REVERT: A 120 MET cc_start: 0.8317 (mmm) cc_final: 0.8058 (mmm) REVERT: B 53 GLU cc_start: 0.8916 (tp30) cc_final: 0.8657 (tp30) REVERT: B 85 ASP cc_start: 0.9346 (m-30) cc_final: 0.9060 (m-30) REVERT: C 91 ASP cc_start: 0.7825 (t70) cc_final: 0.7427 (t0) REVERT: C 109 MET cc_start: 0.6997 (mpp) cc_final: 0.6721 (mtm) REVERT: D 87 SER cc_start: 0.9558 (m) cc_final: 0.9320 (p) REVERT: D 91 ASP cc_start: 0.8785 (t0) cc_final: 0.8541 (t0) REVERT: D 94 GLU cc_start: 0.8871 (tp30) cc_final: 0.8322 (tp30) REVERT: D 98 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8555 (mm110) REVERT: F 84 MET cc_start: 0.8639 (mmm) cc_final: 0.8347 (mmm) REVERT: F 88 TYR cc_start: 0.9153 (m-80) cc_final: 0.8866 (m-80) REVERT: G 91 ASP cc_start: 0.7920 (t70) cc_final: 0.7539 (t0) REVERT: H 94 GLU cc_start: 0.8886 (tp30) cc_final: 0.8233 (tp30) REVERT: H 98 GLN cc_start: 0.9116 (mm-40) cc_final: 0.8576 (mm110) REVERT: H 116 GLU cc_start: 0.8727 (mp0) cc_final: 0.8227 (mp0) outliers start: 12 outliers final: 9 residues processed: 199 average time/residue: 0.1039 time to fit residues: 29.0377 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 : 0.209 ------------------------------------------------------------------------------- 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 D residue 57 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 74 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 38 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.8980 chunk 94 optimal weight: 10.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 overall best weight: 1.5522 ------------------------------------------------------------------------------- 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 E 113 HIS G 74 ASN ** H 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.061093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.042265 restraints weight = 61485.813| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.66 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12647 Z= 0.149 Angle : 0.623 11.575 18329 Z= 0.363 Chirality : 0.041 0.199 2091 Planarity : 0.004 0.034 1312 Dihedral : 31.694 86.464 4073 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.10 % Allowed : 21.77 % 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: 3.30 (0.31), residues: 730 helix: 2.94 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.29 (0.44), residues: 182 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 0.00268 / 0.15 (12647) covalent geometry : angle 0.62261 / 0.36 (18329) hydrogen bonds : bond 0.04570 / 3.19 ( 750) hydrogen bonds : angle 2.92565 / 2.15 ( 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 201 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.331 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 64 LYS cc_start: 0.9305 (mttm) cc_final: 0.8972 (mtmm) REVERT: A 76 GLN cc_start: 0.9183 (tt0) cc_final: 0.8788 (tm-30) REVERT: A 120 MET cc_start: 0.8384 (mmm) cc_final: 0.8151 (mmm) REVERT: B 53 GLU cc_start: 0.8865 (tp30) cc_final: 0.8614 (tp30) REVERT: B 85 ASP cc_start: 0.9314 (m-30) cc_final: 0.9062 (m-30) REVERT: C 91 ASP cc_start: 0.7838 (t70) cc_final: 0.7457 (t0) REVERT: C 109 MET cc_start: 0.7150 (mpp) cc_final: 0.6887 (mtm) REVERT: D 87 SER cc_start: 0.9540 (m) cc_final: 0.9310 (p) REVERT: D 91 ASP cc_start: 0.8763 (t0) cc_final: 0.8520 (t0) REVERT: D 94 GLU cc_start: 0.8826 (tp30) cc_final: 0.8237 (tp30) REVERT: D 98 GLN cc_start: 0.9090 (mm-40) cc_final: 0.8504 (mm110) REVERT: F 84 MET cc_start: 0.8624 (mmm) cc_final: 0.8355 (mmm) REVERT: F 88 TYR cc_start: 0.9139 (m-80) cc_final: 0.8838 (m-80) REVERT: G 91 ASP cc_start: 0.7945 (t70) cc_final: 0.7579 (t0) REVERT: G 108 VAL cc_start: 0.8796 (m) cc_final: 0.8591 (p) REVERT: G 109 MET cc_start: 0.6871 (mpp) cc_final: 0.6509 (mtp) REVERT: H 94 GLU cc_start: 0.8848 (tp30) cc_final: 0.8350 (tp30) REVERT: H 98 GLN cc_start: 0.9103 (mm-40) cc_final: 0.8596 (mm110) REVERT: H 116 GLU cc_start: 0.8739 (mp0) cc_final: 0.8259 (mp0) outliers start: 13 outliers final: 9 residues processed: 191 average time/residue: 0.0998 time to fit residues: 26.9022 Evaluate side-chains 195 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 186 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 F residue 49 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 73 ASP Chi-restraints excluded: chain G residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 41 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 83 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 chunk 67 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.061434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.042665 restraints weight = 61631.642| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 2.70 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12647 Z= 0.136 Angle : 0.622 11.634 18329 Z= 0.363 Chirality : 0.041 0.198 2091 Planarity : 0.004 0.032 1312 Dihedral : 31.630 85.450 4073 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.77 % Allowed : 21.77 % Favored : 76.45 % 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: 3.35 (0.31), residues: 730 helix: 2.96 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.16 (0.45), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 72 TYR 0.028 0.002 TYR B 88 PHE 0.007 0.001 PHE A 67 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (12647) covalent geometry : angle 0.62225 / 0.36 (18329) hydrogen bonds : bond 0.04253 / 2.95 ( 750) hydrogen bonds : angle 2.90845 / 2.15 ( 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 209 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.318 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: 0.9190 (tt0) cc_final: 0.8769 (tm-30) REVERT: A 120 MET cc_start: 0.8312 (mmm) cc_final: 0.8007 (mmm) REVERT: C 91 ASP cc_start: 0.7823 (t70) cc_final: 0.7463 (t0) REVERT: C 109 MET cc_start: 0.7124 (mpp) cc_final: 0.6852 (mtm) REVERT: D 87 SER cc_start: 0.9545 (m) cc_final: 0.9308 (p) REVERT: D 91 ASP cc_start: 0.8818 (t0) cc_final: 0.8565 (t0) REVERT: D 94 GLU cc_start: 0.8863 (tp30) cc_final: 0.8243 (tp30) REVERT: D 98 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8495 (mm110) REVERT: F 84 MET cc_start: 0.8679 (mmm) cc_final: 0.8447 (mmm) REVERT: F 88 TYR cc_start: 0.9157 (m-80) cc_final: 0.8864 (m-80) REVERT: G 72 ARG cc_start: 0.9195 (ttm-80) cc_final: 0.8984 (ttp80) REVERT: G 91 ASP cc_start: 0.8010 (t70) cc_final: 0.7660 (t0) REVERT: G 108 VAL cc_start: 0.8795 (m) cc_final: 0.8564 (p) REVERT: G 109 MET cc_start: 0.6904 (mpp) cc_final: 0.6606 (mtp) REVERT: H 94 GLU cc_start: 0.8864 (tp30) cc_final: 0.8320 (tp30) REVERT: H 98 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8637 (mm110) REVERT: H 116 GLU cc_start: 0.8792 (mp0) cc_final: 0.8293 (mp0) outliers start: 11 outliers final: 9 residues processed: 200 average time/residue: 0.1040 time to fit residues: 29.4539 Evaluate side-chains 202 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 193 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 F residue 49 LEU 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: 2.9990 chunk 37 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 59 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 91 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G 113 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.061479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.042861 restraints weight = 61254.082| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.68 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 12647 Z= 0.138 Angle : 0.635 11.985 18329 Z= 0.367 Chirality : 0.041 0.195 2091 Planarity : 0.003 0.033 1312 Dihedral : 31.594 84.917 4073 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.45 % Allowed : 23.06 % Favored : 75.48 % 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: 3.27 (0.31), residues: 730 helix: 2.88 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.13 (0.46), residues: 184 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 0.00246 / 0.14 (12647) covalent geometry : angle 0.63480 / 0.37 (18329) hydrogen bonds : bond 0.04242 / 2.95 ( 750) hydrogen bonds : angle 2.91598 / 2.14 ( 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 198 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 189 time to evaluate : 0.328 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 64 LYS cc_start: 0.9284 (mttt) cc_final: 0.9054 (mtmm) REVERT: A 76 GLN cc_start: 0.9163 (tt0) cc_final: 0.8779 (tm-30) REVERT: B 53 GLU cc_start: 0.8844 (tp30) cc_final: 0.8569 (tp30) REVERT: C 91 ASP cc_start: 0.7839 (t70) cc_final: 0.7499 (t0) REVERT: D 87 SER cc_start: 0.9556 (m) cc_final: 0.9320 (p) REVERT: D 91 ASP cc_start: 0.8773 (t0) cc_final: 0.8535 (t0) REVERT: D 94 GLU cc_start: 0.8802 (tp30) cc_final: 0.8167 (tp30) REVERT: D 98 GLN cc_start: 0.9101 (mm-40) cc_final: 0.8561 (mm110) REVERT: F 84 MET cc_start: 0.8641 (mmm) cc_final: 0.8427 (mmm) REVERT: F 88 TYR cc_start: 0.9135 (m-80) cc_final: 0.8832 (m-80) REVERT: G 72 ARG cc_start: 0.9140 (ttm-80) cc_final: 0.8896 (ttp80) REVERT: G 91 ASP cc_start: 0.8015 (t70) cc_final: 0.7679 (t0) REVERT: G 108 VAL cc_start: 0.8805 (m) cc_final: 0.8588 (p) REVERT: G 109 MET cc_start: 0.6949 (mpp) cc_final: 0.6656 (mtp) REVERT: H 94 GLU cc_start: 0.8785 (tp30) cc_final: 0.8288 (tp30) REVERT: H 98 GLN cc_start: 0.9081 (mm-40) cc_final: 0.8540 (mm110) REVERT: H 116 GLU cc_start: 0.8767 (mp0) cc_final: 0.8300 (mp0) outliers start: 9 outliers final: 9 residues processed: 191 average time/residue: 0.1087 time to fit residues: 29.3712 Evaluate side-chains 196 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 187 time to evaluate : 0.283 ------------------------------------------------------------------------------- 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 146 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 117 LEU Chi-restraints excluded: chain H residue 146 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 chunk 81 optimal weight: 20.0000 chunk 14 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 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: 4.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.059321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.040683 restraints weight = 62568.305| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.66 r_work: 0.2691 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12647 Z= 0.264 Angle : 0.718 12.087 18329 Z= 0.401 Chirality : 0.045 0.225 2091 Planarity : 0.004 0.034 1312 Dihedral : 31.932 86.689 4073 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.61 % Allowed : 23.06 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.72 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.38 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 30 TYR 0.027 0.002 TYR B 88 PHE 0.010 0.002 PHE G 26 HIS 0.007 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00544 / 0.26 (12647) covalent geometry : angle 0.71756 / 0.40 (18329) hydrogen bonds : bond 0.07282 / 5.11 ( 750) hydrogen bonds : angle 3.28859 / 2.43 ( 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 185 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 175 time to evaluate : 0.323 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: 0.9368 (tt0) cc_final: 0.8915 (tm-30) REVERT: B 53 GLU cc_start: 0.9270 (tp30) cc_final: 0.9022 (tp30) REVERT: C 91 ASP cc_start: 0.7950 (t70) cc_final: 0.7557 (t0) REVERT: D 91 ASP cc_start: 0.9123 (t0) cc_final: 0.8874 (t0) REVERT: D 94 GLU cc_start: 0.9248 (tp30) cc_final: 0.8681 (tp30) REVERT: D 98 GLN cc_start: 0.9436 (mm-40) cc_final: 0.8839 (mm110) REVERT: F 53 GLU cc_start: 0.9253 (tp30) cc_final: 0.8964 (tp30) REVERT: F 84 MET cc_start: 0.9342 (mmm) cc_final: 0.9129 (mmm) REVERT: G 91 ASP cc_start: 0.8058 (t70) cc_final: 0.7713 (t0) REVERT: H 94 GLU cc_start: 0.9198 (tp30) cc_final: 0.8698 (tp30) REVERT: H 98 GLN cc_start: 0.9482 (mm-40) cc_final: 0.8967 (mm110) REVERT: H 116 GLU cc_start: 0.9130 (mp0) cc_final: 0.8680 (mp0) outliers start: 10 outliers final: 8 residues processed: 178 average time/residue: 0.0947 time to fit residues: 23.8443 Evaluate side-chains 175 residues out of total 620 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 167 time to evaluate : 0.211 ------------------------------------------------------------------------------- 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 F residue 49 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain G residue 74 ASN 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: 10.0000 chunk 23 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 20 optimal weight: 0.8980 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: 2.9990 chunk 19 optimal weight: 0.9980 chunk 97 optimal weight: 20.0000 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN G 74 ASN G 90 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.059497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.040542 restraints weight = 62185.647| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.81 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.168 12647 Z= 0.280 Angle : 0.926 59.141 18329 Z= 0.544 Chirality : 0.044 0.244 2091 Planarity : 0.004 0.051 1312 Dihedral : 31.938 86.689 4073 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.45 % Allowed : 23.55 % Favored : 75.00 % Cbeta Deviations : 0.14 % 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: 3.00 (0.31), residues: 730 helix: 2.71 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.38 (0.45), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 30 TYR 0.024 0.002 TYR B 88 PHE 0.009 0.002 PHE G 26 HIS 0.006 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.28 (12647) covalent geometry : angle 0.92576 / 0.54 (18329) hydrogen bonds : bond 0.07265 / 5.11 ( 750) hydrogen bonds : angle 3.30777 / 2.43 ( 1891) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2145.21 seconds wall clock time: 37 minutes 26.82 seconds (2246.82 seconds total)