Starting phenix.real_space_refine on Wed Aug 5 21:57:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k45_62046/08_2026/9k45_62046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k45_62046/08_2026/9k45_62046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9k45_62046/08_2026/9k45_62046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k45_62046/08_2026/9k45_62046.map" model { file = "/net/cci-nas-00/data/ceres_data/9k45_62046/08_2026/9k45_62046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k45_62046/08_2026/9k45_62046.cif" } resolution = 2.71 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= -0.001 sd= 0.051 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 10 5.16 5 C 6577 2.51 5 N 2178 2.21 5 O 2776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11830 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: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 778 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} 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: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 778 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} 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: 2.56, per 1000 atoms: 0.22 Number of scatterers: 11830 At special positions: 0 Unit cell: (122.1, 80.3, 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 10 16.00 P 289 15.00 O 2776 8.00 N 2178 7.00 C 6577 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: 0.92 Conformation dependent library (CDL) restraints added in 256.2 milliseconds 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 74.1% alpha, 2.7% beta 145 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.700A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.643A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.518A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) 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: 3.591A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.662A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 33 Processing helix chain 'C' and resid 37 through 49 removed outlier: 3.813A pdb=" N VAL C 41 " --> pdb=" O PRO C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 85 removed outlier: 3.762A pdb=" N ALA C 60 " --> pdb=" O GLY C 56 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 101 Processing helix chain 'C' and resid 102 through 109 Processing helix chain 'C' and resid 123 through 127 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 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.729A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.634A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.524A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) 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 removed outlier: 3.592A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.710A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 33 Processing helix chain 'G' and resid 37 through 49 removed outlier: 3.831A pdb=" N VAL G 41 " --> pdb=" O PRO G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 56 through 85 removed outlier: 3.767A pdb=" N ALA G 60 " --> pdb=" O GLY G 56 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 101 Processing helix chain 'G' and resid 102 through 109 Processing helix chain 'H' and resid 60 through 72 Processing helix chain 'H' and resid 78 through 107 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 126 through 147 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.134A 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 54 through 55 removed outlier: 6.836A pdb=" N ARG C 54 " --> 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 89 through 90 Processing sheet with id=AA6, first strand: chain 'C' and resid 112 through 113 removed outlier: 6.415A pdb=" N THR C 112 " --> 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: 7.163A 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 54 through 55 removed outlier: 6.730A pdb=" N ARG G 54 " --> 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 89 through 90 403 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 696 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.32 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: 2013 1.33 - 1.45: 4213 1.45 - 1.57: 5816 1.57 - 1.69: 577 1.69 - 1.80: 18 Bond restraints: 12637 Sorted by residual: bond pdb=" O3' DC J -24 " pdb=" P DC J -23 " ideal model delta sigma weight residual 1.607 1.652 -0.045 1.20e-02 6.94e+03 1.40e+01 bond pdb=" O3' DT J 5 " pdb=" P DG J 6 " ideal model delta sigma weight residual 1.607 1.651 -0.044 1.20e-02 6.94e+03 1.37e+01 bond pdb=" C3' DC J -39 " pdb=" C2' DC J -39 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.26e+01 bond pdb=" O3' DA I -9 " pdb=" P DA I -8 " ideal model delta sigma weight residual 1.607 1.644 -0.037 1.20e-02 6.94e+03 9.53e+00 bond pdb=" C3' DT J -21 " pdb=" C2' DT J -21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.07e+00 ... (remaining 12632 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 16503 1.26 - 2.52: 1574 2.52 - 3.78: 211 3.78 - 5.04: 18 5.04 - 6.30: 5 Bond angle restraints: 18311 Sorted by residual: angle pdb=" O4' DA I 69 " pdb=" C4' DA I 69 " pdb=" C3' DA I 69 " ideal model delta sigma weight residual 106.00 102.50 3.50 6.00e-01 2.78e+00 3.39e+01 angle pdb=" N3 DT I -53 " pdb=" C4 DT I -53 " pdb=" O4 DT I -53 " ideal model delta sigma weight residual 119.90 122.72 -2.82 6.00e-01 2.78e+00 2.21e+01 angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.68 -2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" O4' DT I -46 " pdb=" C4' DT I -46 " pdb=" C3' DT I -46 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" N3 DT I 30 " pdb=" C4 DT I 30 " pdb=" O4 DT I 30 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.98e+01 ... (remaining 18306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.07: 4310 18.07 - 36.14: 1106 36.14 - 54.21: 1244 54.21 - 72.28: 243 72.28 - 90.35: 22 Dihedral angle restraints: 6925 sinusoidal: 4777 harmonic: 2148 Sorted by residual: dihedral pdb=" CA THR G 50 " pdb=" C THR G 50 " pdb=" N ALA G 51 " pdb=" CA ALA G 51 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CB GLU G 73 " pdb=" CG GLU G 73 " pdb=" CD GLU G 73 " pdb=" OE1 GLU G 73 " ideal model delta sinusoidal sigma weight residual 0.00 89.72 -89.72 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual 90.00 134.21 -44.21 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 6922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1131 0.031 - 0.062: 655 0.062 - 0.092: 227 0.092 - 0.123: 81 0.123 - 0.154: 5 Chirality restraints: 2099 Sorted by residual: chirality pdb=" P DC J 3 " pdb=" OP1 DC J 3 " pdb=" OP2 DC J 3 " pdb=" O5' DC J 3 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" P DA I -8 " pdb=" OP1 DA I -8 " pdb=" OP2 DA I -8 " pdb=" O5' DA I -8 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.59e-01 chirality pdb=" C3' DA I -8 " pdb=" C4' DA I -8 " pdb=" O3' DA I -8 " pdb=" C2' DA I -8 " both_signs ideal model delta sigma weight residual False -2.73 -2.86 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 2096 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 48 " 0.218 9.50e-02 1.11e+02 9.78e-02 6.13e+00 pdb=" NE ARG C 48 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 48 " 0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG C 48 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG C 48 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 88 " 0.011 2.00e-02 2.50e+03 1.33e-02 3.07e+00 pdb=" CG PHE H 88 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE H 88 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE H 88 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 PHE H 88 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 88 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE H 88 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU H 125 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO H 126 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.023 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1214 2.75 - 3.29: 9691 3.29 - 3.82: 21816 3.82 - 4.36: 26751 4.36 - 4.90: 39014 Nonbonded interactions: 98486 Sorted by model distance: nonbonded pdb=" OG SER G 29 " pdb=" O PHE G 36 " model vdw 2.212 3.040 nonbonded pdb=" OG SER C 29 " pdb=" O PHE C 36 " model vdw 2.228 3.040 nonbonded pdb=" N GLU G 103 " pdb=" OE1 GLU G 103 " model vdw 2.260 3.120 nonbonded pdb=" NH1 ARG B 92 " pdb=" OE1 GLU D 99 " model vdw 2.293 3.120 nonbonded pdb=" NH1 ARG F 92 " pdb=" OE1 GLU H 99 " model vdw 2.317 3.120 ... (remaining 98481 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: 1.500 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.330 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 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 0.045 12637 Z= 0.518 Angle : 0.758 6.295 18311 Z= 0.691 Chirality : 0.043 0.154 2099 Planarity : 0.005 0.098 1298 Dihedral : 28.625 90.350 5537 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 0.96 % Allowed : 21.31 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.50 (0.31), residues: 728 helix: 2.53 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -0.89 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 48 TYR 0.011 0.002 TYR B 51 PHE 0.030 0.001 PHE H 88 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.52 (12637) covalent geometry : angle 0.75802 / 0.69 (18311) hydrogen bonds : bond 0.11164 / 7.21 ( 751) hydrogen bonds : angle 4.41048 / 3.22 ( 1887) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 147 time to evaluate : 0.323 Fit side-chains REVERT: D 91 ASP cc_start: 0.8825 (t70) cc_final: 0.8616 (t0) REVERT: G 46 LYS cc_start: 0.9400 (mtpp) cc_final: 0.9077 (mtmm) REVERT: H 91 ASP cc_start: 0.8831 (t70) cc_final: 0.8629 (t0) outliers start: 6 outliers final: 3 residues processed: 150 average time/residue: 0.8561 time to fit residues: 135.7734 Evaluate side-chains 118 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain G residue 47 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: 2.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS B 75 HIS C 121 HIS D 72 HIS D 107 ASN E 39 HIS E 108 ASN F 75 HIS G 121 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.067880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.048419 restraints weight = 41987.689| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.94 r_work: 0.2847 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12637 Z= 0.155 Angle : 0.658 7.074 18311 Z= 0.386 Chirality : 0.047 0.226 2099 Planarity : 0.005 0.035 1298 Dihedral : 30.926 96.579 4077 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.08 % Allowed : 26.44 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.86 (0.31), residues: 728 helix: 2.77 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.79 (0.39), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 105 TYR 0.013 0.001 TYR B 51 PHE 0.021 0.001 PHE H 88 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.16 (12637) covalent geometry : angle 0.65846 / 0.39 (18311) hydrogen bonds : bond 0.06250 / 4.14 ( 751) hydrogen bonds : angle 3.02848 / 2.22 ( 1887) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 114 time to evaluate : 0.237 Fit side-chains REVERT: C 76 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8576 (tm-30) REVERT: D 91 ASP cc_start: 0.9273 (t70) cc_final: 0.8951 (t0) REVERT: E 94 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8083 (tp30) REVERT: G 46 LYS cc_start: 0.9260 (mtpp) cc_final: 0.8815 (mtmm) REVERT: G 76 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8570 (tm-30) REVERT: H 91 ASP cc_start: 0.9242 (t70) cc_final: 0.8921 (t0) outliers start: 13 outliers final: 4 residues processed: 121 average time/residue: 0.8490 time to fit residues: 108.4638 Evaluate side-chains 112 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 108 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain G residue 50 THR 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 95 optimal weight: 20.0000 chunk 48 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 72 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.067592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.048246 restraints weight = 42602.606| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.95 r_work: 0.2852 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12637 Z= 0.146 Angle : 0.603 6.515 18311 Z= 0.362 Chirality : 0.042 0.202 2099 Planarity : 0.004 0.033 1298 Dihedral : 30.914 96.895 4075 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.37 % Allowed : 25.16 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.31), residues: 728 helix: 3.02 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.71 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.008 0.001 TYR B 51 PHE 0.007 0.001 PHE D 88 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.15 (12637) covalent geometry : angle 0.60256 / 0.36 (18311) hydrogen bonds : bond 0.05529 / 3.68 ( 751) hydrogen bonds : angle 2.81866 / 2.06 ( 1887) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 115 time to evaluate : 0.317 Fit side-chains REVERT: A 94 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8058 (tp30) REVERT: C 48 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8309 (tpp-160) REVERT: C 76 GLU cc_start: 0.8915 (tm-30) cc_final: 0.8609 (tm-30) REVERT: D 85 MET cc_start: 0.9331 (mmm) cc_final: 0.9087 (mmm) REVERT: D 91 ASP cc_start: 0.9254 (t70) cc_final: 0.8941 (t0) REVERT: E 59 GLU cc_start: 0.8336 (pm20) cc_final: 0.8011 (pm20) REVERT: E 94 GLU cc_start: 0.8456 (mm-30) cc_final: 0.7989 (tp30) REVERT: G 46 LYS cc_start: 0.9235 (mtpp) cc_final: 0.8797 (mtmm) REVERT: G 76 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8573 (tm-30) REVERT: H 91 ASP cc_start: 0.9226 (OUTLIER) cc_final: 0.8904 (t0) REVERT: H 116 GLU cc_start: 0.8852 (mp0) cc_final: 0.8458 (mp0) outliers start: 21 outliers final: 12 residues processed: 126 average time/residue: 0.8432 time to fit residues: 112.2229 Evaluate side-chains 126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 48 ARG Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 91 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 81 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 chunk 23 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 49 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.067740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.048833 restraints weight = 42219.413| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.92 r_work: 0.2872 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 12637 Z= 0.139 Angle : 0.596 6.597 18311 Z= 0.357 Chirality : 0.042 0.205 2099 Planarity : 0.004 0.034 1298 Dihedral : 30.876 96.134 4071 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.04 % Allowed : 25.96 % Favored : 70.99 % 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 (0.31), residues: 728 helix: 3.06 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.77 (0.40), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 48 TYR 0.008 0.001 TYR D 63 PHE 0.006 0.001 PHE A 78 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.14 (12637) covalent geometry : angle 0.59596 / 0.36 (18311) hydrogen bonds : bond 0.05139 / 3.42 ( 751) hydrogen bonds : angle 2.71934 / 1.99 ( 1887) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.321 Fit side-chains REVERT: A 59 GLU cc_start: 0.8404 (pm20) cc_final: 0.8075 (pm20) REVERT: A 94 GLU cc_start: 0.8448 (mm-30) cc_final: 0.7973 (tp30) REVERT: C 76 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8620 (tm-30) REVERT: D 58 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7914 (mt-10) REVERT: D 85 MET cc_start: 0.9330 (mmm) cc_final: 0.9080 (mmm) REVERT: D 91 ASP cc_start: 0.9261 (t70) cc_final: 0.8762 (t0) REVERT: D 99 GLU cc_start: 0.9105 (mm-30) cc_final: 0.8895 (mm-30) REVERT: D 147 SER cc_start: 0.8560 (OUTLIER) cc_final: 0.8161 (p) REVERT: E 59 GLU cc_start: 0.8389 (pm20) cc_final: 0.8042 (pm20) REVERT: E 94 GLU cc_start: 0.8442 (mm-30) cc_final: 0.7988 (tp30) REVERT: F 31 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8211 (ptmm) REVERT: G 46 LYS cc_start: 0.9226 (mtpp) cc_final: 0.8788 (mtmm) REVERT: G 76 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8606 (tm-30) REVERT: H 91 ASP cc_start: 0.9234 (t70) cc_final: 0.8901 (t0) REVERT: H 99 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8755 (mm-30) REVERT: H 116 GLU cc_start: 0.8881 (mp0) cc_final: 0.8492 (mp0) outliers start: 19 outliers final: 8 residues processed: 125 average time/residue: 0.8012 time to fit residues: 106.2282 Evaluate side-chains 122 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 112 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 86 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 85 optimal weight: 30.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.067115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.047712 restraints weight = 42685.800| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.96 r_work: 0.2851 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12637 Z= 0.154 Angle : 0.604 6.587 18311 Z= 0.359 Chirality : 0.042 0.207 2099 Planarity : 0.004 0.037 1298 Dihedral : 30.887 93.680 4071 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.88 % Allowed : 25.80 % Favored : 71.31 % 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: 3.41 (0.32), residues: 728 helix: 3.24 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.74 (0.40), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 105 TYR 0.008 0.001 TYR D 63 PHE 0.020 0.001 PHE H 88 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (12637) covalent geometry : angle 0.60350 / 0.36 (18311) hydrogen bonds : bond 0.05485 / 3.64 ( 751) hydrogen bonds : angle 2.77500 / 2.02 ( 1887) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.340 Fit side-chains REVERT: A 59 GLU cc_start: 0.8506 (pm20) cc_final: 0.8167 (pm20) REVERT: A 94 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8041 (tp30) REVERT: C 76 GLU cc_start: 0.8995 (tm-30) cc_final: 0.8540 (tm-30) REVERT: C 104 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8829 (mm-30) REVERT: D 85 MET cc_start: 0.9356 (mmm) cc_final: 0.9102 (mmm) REVERT: D 91 ASP cc_start: 0.9259 (t70) cc_final: 0.8767 (t0) REVERT: D 147 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8176 (p) REVERT: E 59 GLU cc_start: 0.8499 (pm20) cc_final: 0.8146 (pm20) REVERT: E 94 GLU cc_start: 0.8482 (mm-30) cc_final: 0.8017 (tp30) REVERT: F 31 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8346 (ptmm) REVERT: G 76 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8547 (tm-30) REVERT: H 91 ASP cc_start: 0.9250 (OUTLIER) cc_final: 0.8738 (t0) REVERT: H 116 GLU cc_start: 0.8913 (mp0) cc_final: 0.8484 (mp0) outliers start: 18 outliers final: 9 residues processed: 124 average time/residue: 0.8422 time to fit residues: 110.4971 Evaluate side-chains 124 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 112 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 91 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 16 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 83 optimal weight: 20.0000 chunk 87 optimal weight: 30.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.065952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.046484 restraints weight = 42048.766| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 1.95 r_work: 0.2813 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12637 Z= 0.175 Angle : 0.632 7.199 18311 Z= 0.369 Chirality : 0.042 0.208 2099 Planarity : 0.004 0.037 1298 Dihedral : 30.952 91.721 4071 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 4.01 % Allowed : 25.00 % Favored : 70.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.32), residues: 728 helix: 3.17 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.85 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 23 TYR 0.010 0.001 TYR H 63 PHE 0.007 0.001 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.18 (12637) covalent geometry : angle 0.63159 / 0.37 (18311) hydrogen bonds : bond 0.06088 / 4.04 ( 751) hydrogen bonds : angle 2.84326 / 2.07 ( 1887) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.230 Fit side-chains REVERT: A 59 GLU cc_start: 0.8611 (pm20) cc_final: 0.8234 (pm20) REVERT: A 94 GLU cc_start: 0.8585 (mm-30) cc_final: 0.8127 (tp30) REVERT: A 133 GLU cc_start: 0.6742 (OUTLIER) cc_final: 0.6509 (mt-10) REVERT: B 53 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.8554 (mp0) REVERT: C 76 GLU cc_start: 0.9049 (tm-30) cc_final: 0.8593 (tm-30) REVERT: D 91 ASP cc_start: 0.9278 (t70) cc_final: 0.8810 (t0) REVERT: D 99 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8786 (mm-30) REVERT: D 116 GLU cc_start: 0.8762 (mp0) cc_final: 0.8453 (mp0) REVERT: D 147 SER cc_start: 0.8594 (OUTLIER) cc_final: 0.8198 (p) REVERT: E 59 GLU cc_start: 0.8601 (pm20) cc_final: 0.8266 (pm20) REVERT: E 94 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8100 (tp30) REVERT: E 133 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6723 (mt-10) REVERT: F 53 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8558 (mp0) REVERT: G 76 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8571 (tm-30) REVERT: H 91 ASP cc_start: 0.9243 (OUTLIER) cc_final: 0.8758 (t0) REVERT: H 116 GLU cc_start: 0.8916 (mp0) cc_final: 0.8458 (mp0) outliers start: 25 outliers final: 11 residues processed: 128 average time/residue: 0.8204 time to fit residues: 111.2673 Evaluate side-chains 127 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 135 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 20.0000 chunk 94 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 68 optimal weight: 0.0970 chunk 82 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.066202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.047258 restraints weight = 42184.354| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 1.93 r_work: 0.2835 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12637 Z= 0.150 Angle : 0.621 7.733 18311 Z= 0.364 Chirality : 0.042 0.208 2099 Planarity : 0.004 0.056 1298 Dihedral : 30.918 92.492 4071 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.04 % Allowed : 26.60 % Favored : 70.35 % 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: 3.39 (0.32), residues: 728 helix: 3.25 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.84 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 23 TYR 0.009 0.001 TYR D 63 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (12637) covalent geometry : angle 0.62129 / 0.36 (18311) hydrogen bonds : bond 0.05601 / 3.73 ( 751) hydrogen bonds : angle 2.75966 / 2.01 ( 1887) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 111 time to evaluate : 0.229 Fit side-chains REVERT: A 59 GLU cc_start: 0.8607 (pm20) cc_final: 0.8283 (pm20) REVERT: A 94 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8102 (tp30) REVERT: C 76 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8590 (tm-30) REVERT: D 91 ASP cc_start: 0.9274 (t70) cc_final: 0.8804 (t0) REVERT: D 116 GLU cc_start: 0.8816 (mp0) cc_final: 0.8499 (mp0) REVERT: D 147 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8194 (p) REVERT: E 59 GLU cc_start: 0.8597 (pm20) cc_final: 0.8295 (pm20) REVERT: E 94 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8078 (tp30) REVERT: E 120 MET cc_start: 0.8861 (OUTLIER) cc_final: 0.8558 (mtt) REVERT: G 76 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8548 (tm-30) REVERT: H 91 ASP cc_start: 0.9255 (t70) cc_final: 0.8760 (t0) REVERT: H 116 GLU cc_start: 0.8899 (mp0) cc_final: 0.8458 (mp0) outliers start: 19 outliers final: 11 residues processed: 121 average time/residue: 0.7877 time to fit residues: 101.1484 Evaluate side-chains 124 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 136 GLU Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 123 HIS Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 79 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 20.0000 chunk 16 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.066081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.047199 restraints weight = 42165.848| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 1.93 r_work: 0.2833 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12637 Z= 0.153 Angle : 0.620 9.295 18311 Z= 0.364 Chirality : 0.041 0.206 2099 Planarity : 0.004 0.036 1298 Dihedral : 30.847 92.488 4071 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 3.04 % Allowed : 26.92 % Favored : 70.03 % 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: 3.42 (0.32), residues: 728 helix: 3.27 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.82 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 23 TYR 0.008 0.001 TYR H 63 PHE 0.027 0.001 PHE D 88 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (12637) covalent geometry : angle 0.62024 / 0.36 (18311) hydrogen bonds : bond 0.05411 / 3.59 ( 751) hydrogen bonds : angle 2.71310 / 1.98 ( 1887) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 0.220 Fit side-chains REVERT: A 59 GLU cc_start: 0.8663 (pm20) cc_final: 0.8367 (pm20) REVERT: A 94 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8086 (tp30) REVERT: C 76 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8610 (tm-30) REVERT: D 91 ASP cc_start: 0.9277 (OUTLIER) cc_final: 0.8802 (t0) REVERT: D 116 GLU cc_start: 0.8851 (mp0) cc_final: 0.8501 (mp0) REVERT: D 147 SER cc_start: 0.8581 (OUTLIER) cc_final: 0.8191 (p) REVERT: E 59 GLU cc_start: 0.8650 (pm20) cc_final: 0.8343 (pm20) REVERT: E 94 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8074 (tp30) REVERT: E 120 MET cc_start: 0.8862 (OUTLIER) cc_final: 0.8560 (mtt) REVERT: E 133 GLU cc_start: 0.6975 (OUTLIER) cc_final: 0.6745 (mt-10) REVERT: G 76 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8577 (tm-30) REVERT: G 110 LYS cc_start: 0.9111 (mmpt) cc_final: 0.8881 (mmmt) REVERT: H 91 ASP cc_start: 0.9200 (OUTLIER) cc_final: 0.8722 (t0) REVERT: H 116 GLU cc_start: 0.8913 (mp0) cc_final: 0.8465 (mp0) outliers start: 19 outliers final: 11 residues processed: 123 average time/residue: 0.8085 time to fit residues: 105.4540 Evaluate side-chains 130 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 88 PHE Chi-restraints excluded: chain D residue 91 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.8980 chunk 92 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 84 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 30.0000 chunk 93 optimal weight: 20.0000 chunk 72 optimal weight: 30.0000 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.066626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.047846 restraints weight = 42061.104| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.94 r_work: 0.2851 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 12637 Z= 0.143 Angle : 0.620 9.578 18311 Z= 0.365 Chirality : 0.041 0.204 2099 Planarity : 0.004 0.034 1298 Dihedral : 30.809 92.603 4071 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 2.72 % Allowed : 26.92 % Favored : 70.35 % 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: 3.47 (0.31), residues: 728 helix: 3.31 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -0.81 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 48 TYR 0.008 0.001 TYR H 63 PHE 0.046 0.001 PHE D 88 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (12637) covalent geometry : angle 0.62034 / 0.36 (18311) hydrogen bonds : bond 0.05068 / 3.36 ( 751) hydrogen bonds : angle 2.67191 / 1.95 ( 1887) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 113 time to evaluate : 0.333 Fit side-chains REVERT: A 59 GLU cc_start: 0.8671 (pm20) cc_final: 0.8384 (pm20) REVERT: A 94 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8038 (tp30) REVERT: C 76 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8657 (tm-30) REVERT: D 85 MET cc_start: 0.9327 (mmm) cc_final: 0.9096 (mmm) REVERT: D 91 ASP cc_start: 0.9236 (t70) cc_final: 0.8769 (t0) REVERT: D 147 SER cc_start: 0.8572 (OUTLIER) cc_final: 0.8186 (p) REVERT: E 59 GLU cc_start: 0.8671 (pm20) cc_final: 0.8364 (pm20) REVERT: E 94 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8015 (tp30) REVERT: E 120 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8522 (mtt) REVERT: E 133 GLU cc_start: 0.6988 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: G 76 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8565 (tm-30) REVERT: G 110 LYS cc_start: 0.9113 (mmpt) cc_final: 0.8884 (mmmt) REVERT: H 91 ASP cc_start: 0.9198 (OUTLIER) cc_final: 0.8723 (t0) REVERT: H 99 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8648 (mm-30) REVERT: H 116 GLU cc_start: 0.8916 (mp0) cc_final: 0.8492 (mp0) outliers start: 17 outliers final: 10 residues processed: 121 average time/residue: 0.8523 time to fit residues: 109.0550 Evaluate side-chains 125 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 111 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 146 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 14 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 40.0000 chunk 54 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.066775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.048068 restraints weight = 42303.762| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.94 r_work: 0.2860 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 12637 Z= 0.139 Angle : 0.615 9.461 18311 Z= 0.363 Chirality : 0.041 0.202 2099 Planarity : 0.004 0.034 1298 Dihedral : 30.749 91.722 4071 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.40 % Allowed : 26.92 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.48 (0.32), residues: 728 helix: 3.29 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.83 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 23 TYR 0.008 0.001 TYR H 63 PHE 0.029 0.001 PHE H 88 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (12637) covalent geometry : angle 0.61473 / 0.36 (18311) hydrogen bonds : bond 0.04856 / 3.25 ( 751) hydrogen bonds : angle 2.62917 / 1.91 ( 1887) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1456 Ramachandran restraints generated. 728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.289 Fit side-chains REVERT: A 59 GLU cc_start: 0.8687 (pm20) cc_final: 0.8394 (pm20) REVERT: A 94 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8008 (tp30) REVERT: C 76 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8583 (tm-30) REVERT: C 104 GLU cc_start: 0.9032 (mm-30) cc_final: 0.8808 (mm-30) REVERT: D 85 MET cc_start: 0.9381 (mmm) cc_final: 0.9128 (mmm) REVERT: D 91 ASP cc_start: 0.9261 (t70) cc_final: 0.8777 (t0) REVERT: D 99 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8768 (mm-30) REVERT: D 116 GLU cc_start: 0.8802 (mp0) cc_final: 0.8526 (mp0) REVERT: D 147 SER cc_start: 0.8561 (OUTLIER) cc_final: 0.8185 (p) REVERT: E 59 GLU cc_start: 0.8677 (pm20) cc_final: 0.8374 (pm20) REVERT: E 94 GLU cc_start: 0.8454 (mm-30) cc_final: 0.7967 (tp30) REVERT: E 133 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6632 (mt-10) REVERT: G 76 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8591 (tm-30) REVERT: G 110 LYS cc_start: 0.9114 (mmpt) cc_final: 0.8868 (mmmt) REVERT: H 91 ASP cc_start: 0.9188 (OUTLIER) cc_final: 0.8720 (t0) REVERT: H 99 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8640 (mm-30) outliers start: 15 outliers final: 10 residues processed: 121 average time/residue: 0.7810 time to fit residues: 100.0391 Evaluate side-chains 126 residues out of total 624 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 147 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 47 THR Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain H residue 91 ASP Chi-restraints excluded: chain H residue 135 SER Chi-restraints excluded: chain H residue 136 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 95 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 72 optimal weight: 40.0000 chunk 47 optimal weight: 3.9990 chunk 90 optimal weight: 20.0000 chunk 36 optimal weight: 8.9990 chunk 16 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.064914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.045431 restraints weight = 42686.138| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.99 r_work: 0.2778 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8726 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12637 Z= 0.200 Angle : 0.674 9.745 18311 Z= 0.385 Chirality : 0.043 0.214 2099 Planarity : 0.004 0.040 1298 Dihedral : 30.919 87.958 4071 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.56 % Allowed : 26.92 % Favored : 70.51 % 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 (0.32), residues: 728 helix: 3.22 (0.22), residues: 530 sheet: None (None), residues: 0 loop : -1.00 (0.40), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 23 TYR 0.013 0.001 TYR H 63 PHE 0.010 0.002 PHE D 88 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.20 (12637) covalent geometry : angle 0.67407 / 0.39 (18311) hydrogen bonds : bond 0.06938 / 4.59 ( 751) hydrogen bonds : angle 2.93271 / 2.13 ( 1887) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3724.81 seconds wall clock time: 64 minutes 4.44 seconds (3844.44 seconds total)