Starting phenix.real_space_refine on Sat Oct 24 01:36:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mb2_63765/10_2026/9mb2_63765.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mb2_63765/10_2026/9mb2_63765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mb2_63765/10_2026/9mb2_63765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mb2_63765/10_2026/9mb2_63765.map" model { file = "/net/cci-nas-00/data/ceres_data/9mb2_63765/10_2026/9mb2_63765.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mb2_63765/10_2026/9mb2_63765.cif" } resolution = 2.39 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= 0.003 sd= 0.041 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 12 5.16 5 C 6585 2.51 5 N 2235 2.21 5 O 2796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11916 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 781 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 721 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 774 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 730 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Time building chain proxies: 2.54, per 1000 atoms: 0.21 Number of scatterers: 11916 At special positions: 0 Unit cell: (78.44, 121.9, 122.96, 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 288 15.00 O 2796 8.00 N 2235 7.00 C 6585 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: 1.05 Conformation dependent library (CDL) restraints added in 484.6 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1408 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 73.4% alpha, 3.2% beta 133 base pairs and 260 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 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 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.866A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.444A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.523A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.886A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.348A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.911A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.210A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.174A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.728A pdb=" N THR C 101 " --> 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: 6.821A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.278A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 414 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 260 stacking parallelities Total time for adding SS restraints: 2.08 Time building geometry restraints manager: 1.47 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: 2098 1.33 - 1.45: 4223 1.45 - 1.57: 5801 1.57 - 1.68: 576 1.68 - 1.80: 20 Bond restraints: 12718 Sorted by residual: bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DT J 54 " pdb=" C2' DT J 54 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DA J -38 " pdb=" C2' DA J -38 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT J 72 " pdb=" C2' DT J 72 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.61e+00 ... (remaining 12713 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 16042 1.10 - 2.20: 1839 2.20 - 3.30: 491 3.30 - 4.40: 38 4.40 - 5.49: 10 Bond angle restraints: 18420 Sorted by residual: angle pdb=" N3 DT I -42 " pdb=" C4 DT I -42 " pdb=" O4 DT I -42 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT I -59 " pdb=" C4 DT I -59 " pdb=" O4 DT I -59 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT J -23 " pdb=" C4 DT J -23 " pdb=" O4 DT J -23 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT I 41 " pdb=" C4 DT I 41 " pdb=" O4 DT I 41 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.87e+01 ... (remaining 18415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.12: 5304 33.12 - 66.24: 1573 66.24 - 99.37: 19 99.37 - 132.49: 4 132.49 - 165.61: 1 Dihedral angle restraints: 6901 sinusoidal: 4716 harmonic: 2185 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 54.39 165.61 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DC J 34 " pdb=" C3' DC J 34 " pdb=" O3' DC J 34 " pdb=" P DT J 35 " ideal model delta sinusoidal sigma weight residual 220.00 87.81 132.19 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" C4' DA J -38 " pdb=" C3' DA J -38 " pdb=" O3' DA J -38 " pdb=" P DG J -37 " ideal model delta sinusoidal sigma weight residual 220.00 97.85 122.15 1 3.50e+01 8.16e-04 1.20e+01 ... (remaining 6898 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1163 0.032 - 0.065: 556 0.065 - 0.097: 267 0.097 - 0.130: 99 0.130 - 0.162: 11 Chirality restraints: 2096 Sorted by residual: chirality pdb=" CA ALA G 12 " pdb=" N ALA G 12 " pdb=" C ALA G 12 " pdb=" CB ALA G 12 " both_signs ideal model delta sigma weight residual False 2.48 2.65 -0.16 2.00e-01 2.50e+01 6.56e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" C3' DT J 54 " pdb=" C4' DT J 54 " pdb=" O3' DT J 54 " pdb=" C2' DT J 54 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.07e-01 ... (remaining 2093 not shown) Planarity restraints: 1328 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG G 35 " 0.460 9.50e-02 1.11e+02 2.06e-01 2.60e+01 pdb=" NE ARG G 35 " -0.027 2.00e-02 2.50e+03 pdb=" CZ ARG G 35 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG G 35 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG G 35 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.025 2.00e-02 2.50e+03 1.08e-02 3.53e+00 pdb=" N9 DG I 26 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 57 " -0.025 2.00e-02 2.50e+03 1.13e-02 3.50e+00 pdb=" N9 DA I 57 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 57 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 57 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA I 57 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I 57 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 57 " -0.007 2.00e-02 2.50e+03 pdb=" N1 DA I 57 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 57 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 57 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 57 " 0.002 2.00e-02 2.50e+03 ... (remaining 1325 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 613 2.71 - 3.26: 9869 3.26 - 3.81: 22636 3.81 - 4.35: 28186 4.35 - 4.90: 40121 Nonbonded interactions: 101425 Sorted by model distance: nonbonded pdb=" OH TYR H 39 " pdb=" OP2 DA J -53 " model vdw 2.168 3.040 nonbonded pdb=" O SER H 121 " pdb=" OG SER H 121 " model vdw 2.264 3.040 nonbonded pdb=" OG SER H 53 " pdb=" OP2 DC J -54 " model vdw 2.356 3.040 nonbonded pdb=" NH2 ARG G 32 " pdb=" OE1 GLU H 32 " model vdw 2.362 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.389 3.040 ... (remaining 101420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 39 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 30 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.600 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 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:8.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 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 : 0.007 0.039 12718 Z= 0.611 Angle : 0.761 5.494 18420 Z= 0.678 Chirality : 0.048 0.162 2096 Planarity : 0.007 0.206 1328 Dihedral : 28.464 165.612 5493 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.17 % Favored : 97.70 % Rotamer: Outliers : 0.32 % Allowed : 24.68 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.43 (0.31), residues: 739 helix: 2.38 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.73 (0.39), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 20 TYR 0.010 0.002 TYR F 88 PHE 0.007 0.001 PHE D 62 HIS 0.003 0.001 HIS H 106 Details of bonding type rmsd/Z covalent geometry : bond 0.00696 / 0.61 (12718) covalent geometry : angle 0.76144 / 0.68 (18420) hydrogen bonds : bond 0.09919 / 6.55 ( 754) hydrogen bonds : angle 3.32035 / 2.43 ( 1904) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.313 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 113 average time/residue: 1.0309 time to fit residues: 121.6441 Evaluate side-chains 111 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain H residue 39 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45] chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 1.9990 overall best weight: 0.9962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 44 GLN H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.118057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106305 restraints weight = 16278.052| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 0.80 r_work: 0.3401 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.0361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12718 Z= 0.162 Angle : 0.649 7.723 18420 Z= 0.383 Chirality : 0.048 0.266 2096 Planarity : 0.004 0.043 1328 Dihedral : 30.469 167.139 4012 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.76 % Favored : 98.11 % Rotamer: Outliers : 3.18 % Allowed : 23.09 % Favored : 73.73 % 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: 2.87 (0.31), residues: 739 helix: 2.72 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.62 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 17 TYR 0.008 0.001 TYR H 39 PHE 0.006 0.001 PHE D 62 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.16 (12718) covalent geometry : angle 0.64875 / 0.38 (18420) hydrogen bonds : bond 0.05775 / 3.82 ( 754) hydrogen bonds : angle 2.89588 / 2.07 ( 1904) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.287 Fit side-chains REVERT: C 20 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8631 (mtt90) REVERT: C 32 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8386 (tmm160) outliers start: 20 outliers final: 8 residues processed: 116 average time/residue: 0.9994 time to fit residues: 121.2490 Evaluate side-chains 114 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [70, 84, 25, 56, 61, 29, 8, 38, 17, 98, 97] chunk 70 optimal weight: 1.9990 chunk 84 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 98 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 113 HIS ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.119072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.107189 restraints weight = 16305.925| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 0.81 r_work: 0.3414 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12718 Z= 0.148 Angle : 0.615 7.641 18420 Z= 0.368 Chirality : 0.046 0.257 2096 Planarity : 0.004 0.042 1328 Dihedral : 30.556 168.075 4010 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.76 % Favored : 98.11 % Rotamer: Outliers : 2.87 % Allowed : 22.61 % Favored : 74.52 % 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: 3.05 (0.31), residues: 739 helix: 2.86 (0.22), residues: 546 sheet: None (None), residues: 0 loop : -0.58 (0.40), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 129 TYR 0.007 0.001 TYR E 99 PHE 0.006 0.001 PHE D 62 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.15 (12718) covalent geometry : angle 0.61549 / 0.37 (18420) hydrogen bonds : bond 0.05145 / 3.38 ( 754) hydrogen bonds : angle 2.76951 / 1.98 ( 1904) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.308 Fit side-chains REVERT: C 32 ARG cc_start: 0.8597 (ttp-170) cc_final: 0.8387 (tmm160) REVERT: C 51 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8197 (tt) REVERT: E 116 ARG cc_start: 0.8581 (mtp180) cc_final: 0.8169 (ttm110) outliers start: 18 outliers final: 12 residues processed: 116 average time/residue: 1.0545 time to fit residues: 127.7437 Evaluate side-chains 120 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 39 TYR Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [68, 87, 25, 67, 31, 21, 13, 79, 12, 64, 3] chunk 68 optimal weight: 5.9990 chunk 87 optimal weight: 10.0000 chunk 25 optimal weight: 0.3980 chunk 67 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS H 81 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.118202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.106297 restraints weight = 16260.644| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 0.81 r_work: 0.3402 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12718 Z= 0.170 Angle : 0.629 7.900 18420 Z= 0.368 Chirality : 0.048 0.279 2096 Planarity : 0.004 0.044 1328 Dihedral : 30.654 167.913 4010 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.89 % Favored : 97.97 % Rotamer: Outliers : 3.03 % Allowed : 22.45 % Favored : 74.52 % 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: 2.97 (0.30), residues: 739 helix: 2.81 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.65 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 78 TYR 0.010 0.001 TYR F 88 PHE 0.007 0.001 PHE D 62 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (12718) covalent geometry : angle 0.62886 / 0.37 (18420) hydrogen bonds : bond 0.05251 / 3.46 ( 754) hydrogen bonds : angle 2.77985 / 1.99 ( 1904) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 110 time to evaluate : 0.292 Fit side-chains REVERT: C 32 ARG cc_start: 0.8606 (ttp-170) cc_final: 0.8388 (tmm160) REVERT: E 116 ARG cc_start: 0.8597 (mtp180) cc_final: 0.8168 (ttm110) outliers start: 19 outliers final: 10 residues processed: 119 average time/residue: 1.0151 time to fit residues: 126.2920 Evaluate side-chains 120 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 110 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [20, 44, 93, 88, 43, 40, 61, 59, 71, 28, 1] chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 93 optimal weight: 10.0000 chunk 88 optimal weight: 10.9990 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.117402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105674 restraints weight = 16261.389| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 0.79 r_work: 0.3397 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.0630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 12718 Z= 0.186 Angle : 0.640 9.093 18420 Z= 0.371 Chirality : 0.048 0.288 2096 Planarity : 0.004 0.049 1328 Dihedral : 30.692 167.871 4008 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.76 % Favored : 98.11 % Rotamer: Outliers : 3.50 % Allowed : 21.66 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.92 (0.30), residues: 739 helix: 2.77 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.65 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 77 TYR 0.008 0.001 TYR H 39 PHE 0.007 0.001 PHE D 62 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.19 (12718) covalent geometry : angle 0.64002 / 0.37 (18420) hydrogen bonds : bond 0.05367 / 3.53 ( 754) hydrogen bonds : angle 2.77583 / 1.99 ( 1904) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 112 time to evaluate : 0.285 Fit side-chains REVERT: C 20 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8593 (mtt90) REVERT: C 32 ARG cc_start: 0.8599 (ttp-170) cc_final: 0.8384 (tmm160) REVERT: C 91 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.5837 (tp30) REVERT: E 116 ARG cc_start: 0.8606 (mtp180) cc_final: 0.8166 (ttm110) outliers start: 22 outliers final: 14 residues processed: 123 average time/residue: 0.9912 time to fit residues: 127.3956 Evaluate side-chains 127 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [83, 90, 13, 23, 81, 10, 50, 25, 43, 22, 9] chunk 83 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 81 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 9 optimal weight: 0.0050 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.118492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.106614 restraints weight = 16154.023| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 0.80 r_work: 0.3408 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3304 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12718 Z= 0.144 Angle : 0.625 9.020 18420 Z= 0.365 Chirality : 0.047 0.270 2096 Planarity : 0.004 0.046 1328 Dihedral : 30.700 168.110 4008 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.03 % Favored : 97.83 % Rotamer: Outliers : 2.71 % Allowed : 22.61 % Favored : 74.68 % 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: 3.06 (0.31), residues: 739 helix: 2.87 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.61 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 92 TYR 0.007 0.001 TYR E 99 PHE 0.006 0.001 PHE D 62 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (12718) covalent geometry : angle 0.62495 / 0.37 (18420) hydrogen bonds : bond 0.05109 / 3.36 ( 754) hydrogen bonds : angle 2.75041 / 1.97 ( 1904) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.182 Fit side-chains REVERT: C 32 ARG cc_start: 0.8606 (ttp-170) cc_final: 0.8389 (tmm160) REVERT: C 91 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.5840 (tp30) REVERT: E 116 ARG cc_start: 0.8589 (mtp180) cc_final: 0.8160 (ttm110) outliers start: 17 outliers final: 12 residues processed: 118 average time/residue: 0.9748 time to fit residues: 120.1545 Evaluate side-chains 124 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [77, 91, 31, 80, 90, 92, 68, 59, 26, 14, 17] chunk 77 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 80 optimal weight: 9.9990 chunk 90 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.118319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.106446 restraints weight = 16178.695| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 0.80 r_work: 0.3405 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12718 Z= 0.168 Angle : 0.630 10.123 18420 Z= 0.366 Chirality : 0.047 0.279 2096 Planarity : 0.004 0.047 1328 Dihedral : 30.715 168.337 4008 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.89 % Favored : 97.97 % Rotamer: Outliers : 3.18 % Allowed : 22.13 % Favored : 74.68 % 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: 3.00 (0.30), residues: 739 helix: 2.83 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.64 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 17 TYR 0.008 0.001 TYR D 39 PHE 0.006 0.001 PHE D 62 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.17 (12718) covalent geometry : angle 0.62953 / 0.37 (18420) hydrogen bonds : bond 0.05169 / 3.40 ( 754) hydrogen bonds : angle 2.73972 / 1.97 ( 1904) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.301 Fit side-chains REVERT: C 20 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.8589 (mtt90) REVERT: C 32 ARG cc_start: 0.8608 (ttp-170) cc_final: 0.8392 (tmm160) REVERT: C 91 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.5880 (tp30) REVERT: E 116 ARG cc_start: 0.8591 (mtp180) cc_final: 0.8162 (ttm110) outliers start: 20 outliers final: 15 residues processed: 120 average time/residue: 1.0299 time to fit residues: 129.1603 Evaluate side-chains 129 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [1, 10, 42, 74, 46, 66, 19, 53, 99, 94, 92] chunk 1 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 74 optimal weight: 9.9990 chunk 46 optimal weight: 0.4980 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 92 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106703 restraints weight = 16143.569| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 0.80 r_work: 0.3408 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.0696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12718 Z= 0.141 Angle : 0.622 9.378 18420 Z= 0.364 Chirality : 0.046 0.272 2096 Planarity : 0.004 0.046 1328 Dihedral : 30.722 168.477 4008 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.89 % Favored : 97.97 % Rotamer: Outliers : 3.18 % Allowed : 22.13 % Favored : 74.68 % 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: 3.07 (0.30), residues: 739 helix: 2.88 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.62 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 92 TYR 0.007 0.001 TYR F 88 PHE 0.006 0.001 PHE E 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (12718) covalent geometry : angle 0.62203 / 0.36 (18420) hydrogen bonds : bond 0.05084 / 3.34 ( 754) hydrogen bonds : angle 2.73295 / 1.96 ( 1904) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.232 Fit side-chains REVERT: B 45 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7673 (mtt-85) REVERT: C 20 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8587 (mtt90) REVERT: C 32 ARG cc_start: 0.8605 (ttp-170) cc_final: 0.8388 (tmm160) REVERT: C 91 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.5874 (tp30) REVERT: E 116 ARG cc_start: 0.8588 (mtp180) cc_final: 0.8161 (ttm110) outliers start: 20 outliers final: 14 residues processed: 119 average time/residue: 1.0018 time to fit residues: 124.6165 Evaluate side-chains 128 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 20 ARG Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 36 LYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [75, 33, 37, 26, 28, 46, 20, 96, 66, 13, 79] chunk 75 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.0040 chunk 28 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.118549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.106645 restraints weight = 16217.503| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 0.81 r_work: 0.3407 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3303 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.0692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12718 Z= 0.157 Angle : 0.619 7.858 18420 Z= 0.363 Chirality : 0.047 0.272 2096 Planarity : 0.004 0.046 1328 Dihedral : 30.716 168.541 4008 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.14 % Allowed : 1.89 % Favored : 97.97 % Rotamer: Outliers : 2.71 % Allowed : 22.45 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.04 (0.30), residues: 739 helix: 2.86 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.62 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 116 TYR 0.011 0.001 TYR F 88 PHE 0.006 0.001 PHE D 62 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.16 (12718) covalent geometry : angle 0.61895 / 0.36 (18420) hydrogen bonds : bond 0.05090 / 3.35 ( 754) hydrogen bonds : angle 2.72660 / 1.96 ( 1904) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.310 Fit side-chains REVERT: B 45 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7670 (mtt-85) REVERT: C 32 ARG cc_start: 0.8608 (ttp-170) cc_final: 0.8392 (tmm160) REVERT: C 91 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.5876 (tp30) REVERT: E 116 ARG cc_start: 0.8590 (mtp180) cc_final: 0.8163 (ttm110) outliers start: 17 outliers final: 13 residues processed: 117 average time/residue: 1.0423 time to fit residues: 127.3630 Evaluate side-chains 126 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [27, 9, 75, 24, 22, 64, 86, 21, 43, 40, 92] chunk 27 optimal weight: 1.9990 chunk 9 optimal weight: 0.0470 chunk 75 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 40 optimal weight: 0.0870 chunk 92 optimal weight: 10.0000 overall best weight: 0.5656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.118862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.106986 restraints weight = 16202.511| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 0.81 r_work: 0.3412 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12718 Z= 0.134 Angle : 0.613 7.661 18420 Z= 0.361 Chirality : 0.046 0.267 2096 Planarity : 0.004 0.046 1328 Dihedral : 30.725 168.627 4008 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.03 % Favored : 97.83 % Rotamer: Outliers : 2.71 % Allowed : 22.45 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 739 helix: 2.93 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.60 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 20 TYR 0.010 0.001 TYR F 88 PHE 0.006 0.001 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00198 / 0.13 (12718) covalent geometry : angle 0.61345 / 0.36 (18420) hydrogen bonds : bond 0.05001 / 3.29 ( 754) hydrogen bonds : angle 2.72022 / 1.95 ( 1904) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 112 time to evaluate : 0.262 Fit side-chains REVERT: B 45 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7622 (mtt-85) REVERT: C 32 ARG cc_start: 0.8605 (ttp-170) cc_final: 0.8388 (tmm160) REVERT: C 91 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.5832 (tp30) REVERT: E 116 ARG cc_start: 0.8585 (mtp180) cc_final: 0.8161 (ttm110) outliers start: 17 outliers final: 14 residues processed: 119 average time/residue: 1.0271 time to fit residues: 127.6350 Evaluate side-chains 127 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 20 ARG Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 49 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: [42, 15, 59, 44, 22, 34, 30, 31, 6, 89, 48] chunk 42 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.118824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.106934 restraints weight = 16211.801| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 0.81 r_work: 0.3412 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.0713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 12718 Z= 0.142 Angle : 0.614 7.769 18420 Z= 0.360 Chirality : 0.046 0.269 2096 Planarity : 0.004 0.046 1328 Dihedral : 30.717 168.551 4008 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.03 % Favored : 97.83 % Rotamer: Outliers : 2.71 % Allowed : 22.45 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.11 (0.31), residues: 739 helix: 2.91 (0.22), residues: 547 sheet: None (None), residues: 0 loop : -0.60 (0.40), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 77 TYR 0.009 0.001 TYR F 88 PHE 0.005 0.001 PHE E 67 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (12718) covalent geometry : angle 0.61366 / 0.36 (18420) hydrogen bonds : bond 0.04993 / 3.28 ( 754) hydrogen bonds : angle 2.71850 / 1.95 ( 1904) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4164.40 seconds wall clock time: 71 minutes 20.74 seconds (4280.74 seconds total)