Starting phenix.real_space_refine on Fri Jul 3 05:48:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ktq_23026/07_2026/7ktq_23026.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ktq_23026/07_2026/7ktq_23026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7ktq_23026/07_2026/7ktq_23026.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ktq_23026/07_2026/7ktq_23026.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7ktq_23026/07_2026/7ktq_23026.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ktq_23026/07_2026/7ktq_23026.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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 331 5.49 5 S 12 5.16 5 C 6973 2.51 5 N 2384 2.21 5 O 3045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12745 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "G" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 3343 Classifications: {'DNA': 164} Link IDs: {'rna3p': 163} Chain: "J" Number of atoms: 3441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3441 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Time building chain proxies: 2.69, per 1000 atoms: 0.21 Number of scatterers: 12745 At special positions: 0 Unit cell: (76.95, 121.5, 147.15, 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 331 15.00 O 3045 8.00 N 2384 7.00 C 6973 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: 1.02 Conformation dependent library (CDL) restraints added in 330.4 milliseconds 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 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: 32 helices and 10 sheets defined 71.0% alpha, 3.2% beta 117 base pairs and 288 stacking pairs defined. Time for finding SS restraints: 1.80 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.709A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.551A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.559A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 3.652A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.710A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) 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 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.651A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.968A 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 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.552A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.559A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 3.674A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.715A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 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 120 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.904A 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 removed outlier: 6.310A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.173A 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 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.964A 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: 7.192A 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 78 400 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 300 hydrogen bonds 596 hydrogen bond angles 0 basepair planarities 117 basepair parallelities 288 stacking parallelities Total time for adding SS restraints: 2.30 Time building geometry restraints manager: 1.41 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: 2203 1.33 - 1.45: 4715 1.45 - 1.57: 6049 1.57 - 1.69: 661 1.69 - 1.80: 22 Bond restraints: 13650 Sorted by residual: bond pdb=" C3' DA J 83 " pdb=" C2' DA J 83 " ideal model delta sigma weight residual 1.516 1.549 -0.033 8.00e-03 1.56e+04 1.68e+01 bond pdb=" C3' DT J 106 " pdb=" O3' DT J 106 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.57e+01 bond pdb=" C3' DA J 72 " pdb=" O3' DA J 72 " ideal model delta sigma weight residual 1.435 1.386 0.049 1.30e-02 5.92e+03 1.43e+01 bond pdb=" C3' DT J 17 " pdb=" O3' DT J 17 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.29e+01 bond pdb=" C3' DG J 102 " pdb=" O3' DG J 102 " ideal model delta sigma weight residual 1.435 1.388 0.047 1.30e-02 5.92e+03 1.29e+01 ... (remaining 13645 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 17883 1.65 - 3.29: 1803 3.29 - 4.94: 153 4.94 - 6.58: 22 6.58 - 8.23: 4 Bond angle restraints: 19865 Sorted by residual: angle pdb=" O5' DG J 14 " pdb=" C5' DG J 14 " pdb=" C4' DG J 14 " ideal model delta sigma weight residual 109.40 115.24 -5.84 8.00e-01 1.56e+00 5.32e+01 angle pdb=" O5' DT I 146 " pdb=" C5' DT I 146 " pdb=" C4' DT I 146 " ideal model delta sigma weight residual 109.40 114.69 -5.29 8.00e-01 1.56e+00 4.38e+01 angle pdb=" O5' DC I 64 " pdb=" C5' DC I 64 " pdb=" C4' DC I 64 " ideal model delta sigma weight residual 109.40 114.36 -4.96 8.00e-01 1.56e+00 3.84e+01 angle pdb=" O5' DG I 77 " pdb=" C5' DG I 77 " pdb=" C4' DG I 77 " ideal model delta sigma weight residual 109.40 113.51 -4.11 8.00e-01 1.56e+00 2.65e+01 angle pdb=" O4' DT I 58 " pdb=" C4' DT I 58 " pdb=" C3' DT I 58 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.61e+01 ... (remaining 19860 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 5693 35.95 - 71.89: 1623 71.89 - 107.84: 21 107.84 - 143.79: 0 143.79 - 179.74: 5 Dihedral angle restraints: 7342 sinusoidal: 5160 harmonic: 2182 Sorted by residual: dihedral pdb=" C4' DC I 3 " pdb=" C3' DC I 3 " pdb=" O3' DC I 3 " pdb=" P DC I 4 " ideal model delta sinusoidal sigma weight residual -140.00 39.74 -179.74 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG I 104 " pdb=" C3' DG I 104 " pdb=" O3' DG I 104 " pdb=" P DC I 105 " ideal model delta sinusoidal sigma weight residual 220.00 40.45 179.55 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 106 " pdb=" C3' DT J 106 " pdb=" O3' DT J 106 " pdb=" P DG J 107 " ideal model delta sinusoidal sigma weight residual 220.00 42.30 177.70 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7339 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1597 0.059 - 0.118: 567 0.118 - 0.177: 91 0.177 - 0.236: 5 0.236 - 0.295: 2 Chirality restraints: 2262 Sorted by residual: chirality pdb=" CG LEU G 115 " pdb=" CB LEU G 115 " pdb=" CD1 LEU G 115 " pdb=" CD2 LEU G 115 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" C1' DG J 66 " pdb=" O4' DG J 66 " pdb=" C2' DG J 66 " pdb=" N9 DG J 66 " both_signs ideal model delta sigma weight residual False 2.43 2.18 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' DG I 104 " pdb=" C4' DG I 104 " pdb=" O3' DG I 104 " pdb=" C2' DG I 104 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 2259 not shown) Planarity restraints: 1368 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 106 " 0.005 2.00e-02 2.50e+03 3.37e-02 2.55e+01 pdb=" N1 DC I 106 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DC I 106 " 0.083 2.00e-02 2.50e+03 pdb=" O2 DC I 106 " -0.045 2.00e-02 2.50e+03 pdb=" N3 DC I 106 " -0.009 2.00e-02 2.50e+03 pdb=" C4 DC I 106 " 0.016 2.00e-02 2.50e+03 pdb=" N4 DC I 106 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DC I 106 " -0.004 2.00e-02 2.50e+03 pdb=" C6 DC I 106 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 87 " -0.043 2.00e-02 2.50e+03 2.87e-02 1.86e+01 pdb=" N1 DC J 87 " 0.068 2.00e-02 2.50e+03 pdb=" C2 DC J 87 " -0.027 2.00e-02 2.50e+03 pdb=" O2 DC J 87 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DC J 87 " 0.002 2.00e-02 2.50e+03 pdb=" C4 DC J 87 " -0.005 2.00e-02 2.50e+03 pdb=" N4 DC J 87 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DC J 87 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC J 87 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS H 106 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C HIS H 106 " 0.073 2.00e-02 2.50e+03 pdb=" O HIS H 106 " -0.027 2.00e-02 2.50e+03 pdb=" N ALA H 107 " -0.025 2.00e-02 2.50e+03 ... (remaining 1365 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1483 2.74 - 3.28: 10850 3.28 - 3.82: 24023 3.82 - 4.36: 29764 4.36 - 4.90: 41980 Nonbonded interactions: 108100 Sorted by model distance: nonbonded pdb=" OE1 GLU B 74 " pdb=" NH2 ARG D 96 " model vdw 2.201 3.120 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.248 3.040 nonbonded pdb=" C2' DA J 20 " pdb=" C7 DT J 21 " model vdw 2.274 3.860 nonbonded pdb=" OE1 GLU F 74 " pdb=" NH2 ARG H 96 " model vdw 2.295 3.120 nonbonded pdb=" O6 DG I 44 " pdb=" N4 DC J 124 " model vdw 2.313 3.120 ... (remaining 108095 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 38 through 133) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 14 through 117) 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=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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.300 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 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 : 0.008 0.067 13650 Z= 0.675 Angle : 0.977 8.228 19865 Z= 0.811 Chirality : 0.058 0.295 2262 Planarity : 0.009 0.043 1368 Dihedral : 29.268 179.736 5934 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.92 % 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 (0.24), residues: 736 helix: -1.35 (0.18), residues: 532 sheet: None (None), residues: 0 loop : -1.86 (0.34), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 83 TYR 0.015 0.002 TYR F 98 PHE 0.016 0.003 PHE C 25 HIS 0.012 0.002 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00850 / 0.68 (13650) covalent geometry : angle 0.97724 / 0.81 (19865) hydrogen bonds : bond 0.14041 / 9.31 ( 700) hydrogen bonds : angle 6.28309 / 4.44 ( 1796) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.310 Fit side-chains REVERT: A 97 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7634 (mt-10) REVERT: D 30 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7046 (ptm160) REVERT: D 65 ASP cc_start: 0.8839 (t0) cc_final: 0.8598 (t0) REVERT: D 113 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8093 (tttp) REVERT: D 116 THR cc_start: 0.8694 (m) cc_final: 0.8245 (p) REVERT: D 117 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8656 (ttmt) REVERT: E 90 MET cc_start: 0.8070 (tpp) cc_final: 0.7567 (mmm) REVERT: F 35 ARG cc_start: 0.8135 (mtm180) cc_final: 0.7851 (mtm110) REVERT: G 36 LYS cc_start: 0.8465 (pttp) cc_final: 0.7836 (mmmt) REVERT: G 75 LYS cc_start: 0.8463 (mttt) cc_final: 0.8194 (mtpt) REVERT: G 95 LYS cc_start: 0.8683 (tptt) cc_final: 0.8434 (tptt) REVERT: H 40 LYS cc_start: 0.8557 (mttm) cc_final: 0.8255 (mttt) REVERT: H 64 ASN cc_start: 0.9031 (m-40) cc_final: 0.8809 (m-40) REVERT: H 117 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8436 (tppt) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.2036 time to fit residues: 48.1942 Evaluate side-chains 134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 134 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.0770 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN B 93 GLN D 81 ASN F 27 GLN G 38 ASN G 73 ASN G 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.157285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.108185 restraints weight = 17665.692| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 0.93 r_work: 0.3020 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2897 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13650 Z= 0.156 Angle : 0.641 6.750 19865 Z= 0.375 Chirality : 0.046 0.259 2262 Planarity : 0.005 0.043 1368 Dihedral : 32.950 179.588 4452 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.96 % Allowed : 9.44 % Favored : 89.60 % 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: 0.95 (0.29), residues: 736 helix: 1.30 (0.21), residues: 541 sheet: None (None), residues: 0 loop : -1.21 (0.37), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 76 TYR 0.011 0.002 TYR G 57 PHE 0.010 0.001 PHE C 25 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.16 (13650) covalent geometry : angle 0.64135 / 0.38 (19865) hydrogen bonds : bond 0.06507 / 4.24 ( 700) hydrogen bonds : angle 3.26964 / 2.35 ( 1796) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.312 Fit side-chains REVERT: C 20 ARG cc_start: 0.8930 (ttm170) cc_final: 0.8718 (ttm170) REVERT: D 30 ARG cc_start: 0.7530 (mtt180) cc_final: 0.6914 (ptm160) REVERT: D 80 TYR cc_start: 0.8639 (m-10) cc_final: 0.7726 (m-10) REVERT: D 113 LYS cc_start: 0.8808 (ttpt) cc_final: 0.8399 (tttp) REVERT: D 116 THR cc_start: 0.8851 (m) cc_final: 0.8329 (p) REVERT: D 117 LYS cc_start: 0.8961 (ttmt) cc_final: 0.8741 (ttmt) REVERT: E 90 MET cc_start: 0.8775 (tpp) cc_final: 0.8429 (mmm) REVERT: F 35 ARG cc_start: 0.8670 (mtm180) cc_final: 0.8328 (mtm110) REVERT: F 68 ASP cc_start: 0.9295 (m-30) cc_final: 0.9019 (m-30) REVERT: G 35 ARG cc_start: 0.8188 (mtp-110) cc_final: 0.7940 (mtm110) REVERT: G 36 LYS cc_start: 0.8647 (pttp) cc_final: 0.8091 (mmmt) REVERT: G 75 LYS cc_start: 0.8560 (mttt) cc_final: 0.8262 (mtpt) REVERT: G 95 LYS cc_start: 0.9049 (tptt) cc_final: 0.8757 (tptt) REVERT: H 40 LYS cc_start: 0.8758 (mttm) cc_final: 0.8529 (mttt) outliers start: 6 outliers final: 3 residues processed: 141 average time/residue: 0.1436 time to fit residues: 27.2966 Evaluate side-chains 127 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 58 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 27 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 93 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 25 ASN B 93 GLN F 93 GLN G 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.155508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105790 restraints weight = 17893.728| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 0.97 r_work: 0.3030 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13650 Z= 0.168 Angle : 0.599 6.005 19865 Z= 0.351 Chirality : 0.044 0.278 2262 Planarity : 0.004 0.042 1368 Dihedral : 32.824 179.551 4452 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.44 % Allowed : 9.76 % Favored : 88.80 % 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: 2.01 (0.30), residues: 736 helix: 2.12 (0.22), residues: 541 sheet: None (None), residues: 0 loop : -0.96 (0.39), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 42 TYR 0.011 0.002 TYR F 98 PHE 0.012 0.002 PHE C 25 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.17 (13650) covalent geometry : angle 0.59873 / 0.35 (19865) hydrogen bonds : bond 0.05932 / 3.97 ( 700) hydrogen bonds : angle 3.08591 / 2.24 ( 1796) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 126 time to evaluate : 0.315 Fit side-chains REVERT: C 20 ARG cc_start: 0.8997 (ttm170) cc_final: 0.8791 (ttm170) REVERT: D 30 ARG cc_start: 0.7667 (mtt180) cc_final: 0.6954 (ptm160) REVERT: D 80 TYR cc_start: 0.8664 (m-10) cc_final: 0.7934 (m-10) REVERT: D 113 LYS cc_start: 0.8864 (ttpt) cc_final: 0.8504 (tttp) REVERT: D 116 THR cc_start: 0.8949 (m) cc_final: 0.8335 (p) REVERT: D 117 LYS cc_start: 0.8917 (ttmt) cc_final: 0.8703 (ttmt) REVERT: E 90 MET cc_start: 0.8779 (tpp) cc_final: 0.8540 (mmm) REVERT: F 35 ARG cc_start: 0.8778 (mmm160) cc_final: 0.8458 (mtm110) REVERT: F 68 ASP cc_start: 0.9301 (m-30) cc_final: 0.9008 (m-30) REVERT: F 84 MET cc_start: 0.9046 (mmp) cc_final: 0.8821 (mmm) REVERT: G 35 ARG cc_start: 0.8199 (mtp-110) cc_final: 0.7947 (mtm110) REVERT: G 36 LYS cc_start: 0.8554 (pttp) cc_final: 0.8093 (mmmt) REVERT: G 95 LYS cc_start: 0.8984 (tptt) cc_final: 0.8729 (tptt) REVERT: G 110 ASN cc_start: 0.8507 (t0) cc_final: 0.8208 (t0) REVERT: H 39 TYR cc_start: 0.8448 (t80) cc_final: 0.7699 (t80) REVERT: H 40 LYS cc_start: 0.8755 (mttm) cc_final: 0.8536 (mttt) outliers start: 9 outliers final: 7 residues processed: 130 average time/residue: 0.1491 time to fit residues: 26.0768 Evaluate side-chains 125 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 97 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 76 optimal weight: 10.0000 chunk 12 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN C 84 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.156143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.106685 restraints weight = 17726.692| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 0.92 r_work: 0.3032 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 13650 Z= 0.142 Angle : 0.562 6.095 19865 Z= 0.334 Chirality : 0.042 0.284 2262 Planarity : 0.004 0.041 1368 Dihedral : 32.516 179.186 4452 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.64 % Allowed : 11.20 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.30), residues: 736 helix: 2.64 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -0.77 (0.39), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 42 TYR 0.009 0.001 TYR G 57 PHE 0.007 0.001 PHE C 25 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.14 (13650) covalent geometry : angle 0.56189 / 0.33 (19865) hydrogen bonds : bond 0.05233 / 3.47 ( 700) hydrogen bonds : angle 2.90653 / 2.11 ( 1796) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 129 time to evaluate : 0.327 Fit side-chains REVERT: C 20 ARG cc_start: 0.8983 (ttm170) cc_final: 0.8768 (ttm170) REVERT: D 30 ARG cc_start: 0.7793 (mtt180) cc_final: 0.6826 (ptp-170) REVERT: D 80 TYR cc_start: 0.8637 (m-10) cc_final: 0.7814 (m-10) REVERT: D 113 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8616 (tttp) REVERT: D 116 THR cc_start: 0.8932 (m) cc_final: 0.8325 (p) REVERT: E 90 MET cc_start: 0.8746 (tpp) cc_final: 0.8520 (mmm) REVERT: E 122 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8151 (mtmt) REVERT: F 35 ARG cc_start: 0.8753 (mmm160) cc_final: 0.8446 (mtm110) REVERT: F 68 ASP cc_start: 0.9290 (m-30) cc_final: 0.8969 (m-30) REVERT: G 35 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7959 (mtm110) REVERT: G 36 LYS cc_start: 0.8557 (pttp) cc_final: 0.8118 (mmmt) REVERT: G 95 LYS cc_start: 0.8998 (tptt) cc_final: 0.8776 (tptt) REVERT: G 110 ASN cc_start: 0.8575 (t0) cc_final: 0.8267 (t0) REVERT: H 39 TYR cc_start: 0.8470 (t80) cc_final: 0.7678 (t80) REVERT: H 99 LEU cc_start: 0.9445 (mt) cc_final: 0.9235 (mt) outliers start: 4 outliers final: 3 residues processed: 130 average time/residue: 0.1528 time to fit residues: 26.5797 Evaluate side-chains 127 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 124 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 58 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN C 84 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.155299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.105779 restraints weight = 17821.461| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 0.93 r_work: 0.3008 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13650 Z= 0.148 Angle : 0.562 6.150 19865 Z= 0.333 Chirality : 0.042 0.286 2262 Planarity : 0.004 0.039 1368 Dihedral : 32.324 178.806 4452 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.96 % Allowed : 11.20 % Favored : 87.84 % 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: 2.85 (0.31), residues: 736 helix: 2.77 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.79 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.010 0.001 TYR F 51 PHE 0.009 0.001 PHE C 25 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.15 (13650) covalent geometry : angle 0.56249 / 0.33 (19865) hydrogen bonds : bond 0.05307 / 3.58 ( 700) hydrogen bonds : angle 2.90200 / 2.12 ( 1796) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 128 time to evaluate : 0.283 Fit side-chains REVERT: B 26 ILE cc_start: 0.9100 (tp) cc_final: 0.8862 (tp) REVERT: C 20 ARG cc_start: 0.9022 (ttm170) cc_final: 0.8808 (ttm170) REVERT: D 30 ARG cc_start: 0.7914 (mtt180) cc_final: 0.6917 (ptp-170) REVERT: D 113 LYS cc_start: 0.8893 (ttpt) cc_final: 0.8638 (tttp) REVERT: D 116 THR cc_start: 0.8923 (m) cc_final: 0.8325 (p) REVERT: E 90 MET cc_start: 0.8754 (tpp) cc_final: 0.8545 (mmm) REVERT: E 122 LYS cc_start: 0.8435 (mtmt) cc_final: 0.8143 (mtmt) REVERT: F 35 ARG cc_start: 0.8762 (mmm160) cc_final: 0.8449 (mtm110) REVERT: F 84 MET cc_start: 0.9143 (mmt) cc_final: 0.8511 (mmm) REVERT: G 35 ARG cc_start: 0.8254 (mtp-110) cc_final: 0.7992 (mtm110) REVERT: G 36 LYS cc_start: 0.8629 (pttp) cc_final: 0.8204 (mmmt) REVERT: G 95 LYS cc_start: 0.8992 (tptt) cc_final: 0.8768 (tptt) REVERT: H 39 TYR cc_start: 0.8569 (t80) cc_final: 0.7728 (t80) REVERT: H 99 LEU cc_start: 0.9432 (mt) cc_final: 0.9223 (mt) outliers start: 6 outliers final: 5 residues processed: 131 average time/residue: 0.1508 time to fit residues: 26.5742 Evaluate side-chains 127 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 122 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 61 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.152592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.101805 restraints weight = 17787.347| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.16 r_work: 0.2890 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13650 Z= 0.186 Angle : 0.595 7.202 19865 Z= 0.344 Chirality : 0.044 0.291 2262 Planarity : 0.005 0.038 1368 Dihedral : 32.318 179.448 4452 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.76 % Allowed : 11.36 % Favored : 86.88 % 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: 2.70 (0.31), residues: 736 helix: 2.68 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.90 (0.41), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 88 TYR 0.013 0.002 TYR F 51 PHE 0.010 0.002 PHE C 25 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (13650) covalent geometry : angle 0.59513 / 0.34 (19865) hydrogen bonds : bond 0.05618 / 3.78 ( 700) hydrogen bonds : angle 2.97623 / 2.17 ( 1796) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.312 Fit side-chains REVERT: B 26 ILE cc_start: 0.9134 (tp) cc_final: 0.8931 (tp) REVERT: C 20 ARG cc_start: 0.9017 (ttm170) cc_final: 0.8802 (ttm170) REVERT: D 30 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7120 (ptp-170) REVERT: D 37 TYR cc_start: 0.9224 (m-80) cc_final: 0.8912 (m-80) REVERT: D 113 LYS cc_start: 0.8889 (ttpt) cc_final: 0.8679 (tttp) REVERT: E 90 MET cc_start: 0.8867 (tpp) cc_final: 0.8626 (mmm) REVERT: E 122 LYS cc_start: 0.8515 (mtmt) cc_final: 0.8263 (mtmt) REVERT: E 129 ARG cc_start: 0.8402 (tpt90) cc_final: 0.8091 (tpt90) REVERT: F 35 ARG cc_start: 0.8888 (mmm160) cc_final: 0.8464 (mtm110) REVERT: F 68 ASP cc_start: 0.9234 (m-30) cc_final: 0.8985 (m-30) REVERT: G 35 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7974 (mtm110) REVERT: G 36 LYS cc_start: 0.8699 (pttp) cc_final: 0.8196 (mmmt) REVERT: H 33 SER cc_start: 0.9160 (t) cc_final: 0.8943 (p) REVERT: H 39 TYR cc_start: 0.8751 (t80) cc_final: 0.7621 (t80) outliers start: 11 outliers final: 8 residues processed: 132 average time/residue: 0.1518 time to fit residues: 26.6481 Evaluate side-chains 129 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 73 optimal weight: 10.0000 chunk 72 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 7 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN D 92 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.153062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.102452 restraints weight = 17760.466| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.16 r_work: 0.2944 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13650 Z= 0.143 Angle : 0.576 6.839 19865 Z= 0.336 Chirality : 0.043 0.286 2262 Planarity : 0.004 0.035 1368 Dihedral : 32.295 179.263 4452 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.60 % Allowed : 11.52 % Favored : 86.88 % 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: 736 helix: 2.80 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.87 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 83 TYR 0.012 0.001 TYR F 51 PHE 0.008 0.001 PHE C 25 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (13650) covalent geometry : angle 0.57609 / 0.34 (19865) hydrogen bonds : bond 0.05406 / 3.63 ( 700) hydrogen bonds : angle 2.95177 / 2.15 ( 1796) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 0.305 Fit side-chains REVERT: B 26 ILE cc_start: 0.9132 (tp) cc_final: 0.8909 (tp) REVERT: C 20 ARG cc_start: 0.9004 (ttm170) cc_final: 0.8781 (ttm170) REVERT: D 30 ARG cc_start: 0.7995 (mtt180) cc_final: 0.7141 (ptp-170) REVERT: D 37 TYR cc_start: 0.9233 (m-80) cc_final: 0.8924 (m-80) REVERT: D 113 LYS cc_start: 0.8876 (ttpt) cc_final: 0.8651 (tttp) REVERT: E 90 MET cc_start: 0.8876 (tpp) cc_final: 0.8633 (mmm) REVERT: E 122 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8259 (mtmt) REVERT: E 129 ARG cc_start: 0.8487 (tpt90) cc_final: 0.8149 (tpt90) REVERT: F 35 ARG cc_start: 0.8856 (mmm160) cc_final: 0.8445 (mtm110) REVERT: F 68 ASP cc_start: 0.9225 (m-30) cc_final: 0.8957 (m-30) REVERT: G 35 ARG cc_start: 0.8230 (mtp-110) cc_final: 0.7947 (mtm110) REVERT: G 36 LYS cc_start: 0.8679 (pttp) cc_final: 0.8217 (mmmt) REVERT: G 38 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8425 (m110) REVERT: H 33 SER cc_start: 0.9150 (t) cc_final: 0.8938 (p) REVERT: H 39 TYR cc_start: 0.8711 (t80) cc_final: 0.7612 (t80) outliers start: 10 outliers final: 8 residues processed: 129 average time/residue: 0.1498 time to fit residues: 25.9265 Evaluate side-chains 132 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 123 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 82 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 6 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.0670 chunk 45 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN D 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.153355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.102792 restraints weight = 17679.407| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.15 r_work: 0.2915 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.2632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13650 Z= 0.136 Angle : 0.566 6.658 19865 Z= 0.332 Chirality : 0.042 0.287 2262 Planarity : 0.004 0.035 1368 Dihedral : 32.262 179.093 4452 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.28 % Allowed : 11.84 % Favored : 86.88 % 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 (0.31), residues: 736 helix: 2.84 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.85 (0.42), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 129 TYR 0.012 0.001 TYR F 51 PHE 0.007 0.001 PHE A 67 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.14 (13650) covalent geometry : angle 0.56568 / 0.33 (19865) hydrogen bonds : bond 0.05276 / 3.54 ( 700) hydrogen bonds : angle 2.91526 / 2.13 ( 1796) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 124 time to evaluate : 0.322 Fit side-chains REVERT: B 26 ILE cc_start: 0.9120 (tp) cc_final: 0.8898 (tp) REVERT: C 20 ARG cc_start: 0.8998 (ttm170) cc_final: 0.8778 (ttm170) REVERT: D 30 ARG cc_start: 0.7978 (mtt180) cc_final: 0.7118 (ptp-170) REVERT: D 37 TYR cc_start: 0.9223 (m-80) cc_final: 0.8918 (m-80) REVERT: D 113 LYS cc_start: 0.8879 (ttpt) cc_final: 0.8669 (tttp) REVERT: E 90 MET cc_start: 0.8868 (tpp) cc_final: 0.8627 (mmm) REVERT: E 122 LYS cc_start: 0.8527 (mtmt) cc_final: 0.8263 (mtmt) REVERT: E 129 ARG cc_start: 0.8499 (tpt90) cc_final: 0.8166 (tpt90) REVERT: F 35 ARG cc_start: 0.8858 (mmm160) cc_final: 0.8449 (mtm110) REVERT: F 68 ASP cc_start: 0.9223 (m-30) cc_final: 0.8954 (m-30) REVERT: G 35 ARG cc_start: 0.8230 (mtp-110) cc_final: 0.7944 (mtm110) REVERT: G 36 LYS cc_start: 0.8682 (pttp) cc_final: 0.8221 (mmmt) REVERT: G 38 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8409 (m110) REVERT: H 33 SER cc_start: 0.9151 (t) cc_final: 0.8936 (p) REVERT: H 39 TYR cc_start: 0.8709 (t80) cc_final: 0.7618 (t80) outliers start: 8 outliers final: 7 residues processed: 128 average time/residue: 0.1531 time to fit residues: 26.3546 Evaluate side-chains 130 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 9 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.152801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.102231 restraints weight = 17795.628| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.15 r_work: 0.2928 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13650 Z= 0.163 Angle : 0.568 6.693 19865 Z= 0.334 Chirality : 0.042 0.290 2262 Planarity : 0.004 0.036 1368 Dihedral : 32.138 179.757 4452 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.12 % Allowed : 11.84 % Favored : 87.04 % 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: 2.93 (0.31), residues: 736 helix: 2.83 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.81 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 83 TYR 0.014 0.001 TYR F 51 PHE 0.009 0.001 PHE F 100 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (13650) covalent geometry : angle 0.56800 / 0.33 (19865) hydrogen bonds : bond 0.05357 / 3.61 ( 700) hydrogen bonds : angle 2.91447 / 2.13 ( 1796) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.356 Fit side-chains REVERT: B 26 ILE cc_start: 0.9114 (tp) cc_final: 0.8894 (tp) REVERT: B 88 TYR cc_start: 0.9122 (m-10) cc_final: 0.8532 (m-80) REVERT: C 20 ARG cc_start: 0.9050 (ttm170) cc_final: 0.8833 (ttm170) REVERT: D 30 ARG cc_start: 0.7888 (mtt180) cc_final: 0.6936 (ptp-170) REVERT: D 37 TYR cc_start: 0.9250 (m-80) cc_final: 0.8957 (m-80) REVERT: D 113 LYS cc_start: 0.8881 (ttpt) cc_final: 0.8662 (tttp) REVERT: E 90 MET cc_start: 0.8860 (tpp) cc_final: 0.8589 (mmm) REVERT: E 122 LYS cc_start: 0.8537 (mtmt) cc_final: 0.8255 (mtmt) REVERT: E 129 ARG cc_start: 0.8510 (tpt90) cc_final: 0.8175 (tpt90) REVERT: F 35 ARG cc_start: 0.8854 (mmm160) cc_final: 0.8449 (mtm110) REVERT: F 68 ASP cc_start: 0.9223 (m-30) cc_final: 0.8947 (m-30) REVERT: G 35 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.7993 (mtm110) REVERT: G 36 LYS cc_start: 0.8651 (pttp) cc_final: 0.8236 (mmmt) REVERT: G 38 ASN cc_start: 0.8812 (OUTLIER) cc_final: 0.8389 (m110) REVERT: H 33 SER cc_start: 0.9165 (t) cc_final: 0.8947 (p) REVERT: H 39 TYR cc_start: 0.8822 (t80) cc_final: 0.8523 (t80) outliers start: 7 outliers final: 5 residues processed: 130 average time/residue: 0.1558 time to fit residues: 27.0358 Evaluate side-chains 131 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 125 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 92 optimal weight: 9.9990 chunk 100 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 44 optimal weight: 0.0060 chunk 23 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.153169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.102687 restraints weight = 17834.553| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.15 r_work: 0.2938 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13650 Z= 0.150 Angle : 0.560 6.631 19865 Z= 0.330 Chirality : 0.042 0.284 2262 Planarity : 0.004 0.040 1368 Dihedral : 32.113 179.688 4452 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.12 % Allowed : 12.16 % Favored : 86.72 % 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: 3.02 (0.31), residues: 736 helix: 2.89 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.76 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 83 TYR 0.012 0.001 TYR F 51 PHE 0.007 0.001 PHE D 62 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (13650) covalent geometry : angle 0.56030 / 0.33 (19865) hydrogen bonds : bond 0.05193 / 3.50 ( 700) hydrogen bonds : angle 2.89882 / 2.12 ( 1796) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1472 Ramachandran restraints generated. 736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.352 Fit side-chains REVERT: B 26 ILE cc_start: 0.9102 (tp) cc_final: 0.8883 (tp) REVERT: C 20 ARG cc_start: 0.9041 (ttm170) cc_final: 0.8820 (ttm170) REVERT: D 30 ARG cc_start: 0.7910 (mtt180) cc_final: 0.6894 (ptp-170) REVERT: D 37 TYR cc_start: 0.9239 (m-80) cc_final: 0.8945 (m-80) REVERT: D 113 LYS cc_start: 0.8909 (ttpt) cc_final: 0.8690 (tttp) REVERT: E 90 MET cc_start: 0.8845 (tpp) cc_final: 0.8580 (mmm) REVERT: E 122 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8249 (mtmt) REVERT: E 129 ARG cc_start: 0.8511 (tpt90) cc_final: 0.8150 (tpt90) REVERT: F 35 ARG cc_start: 0.8839 (mmm160) cc_final: 0.8439 (mtm110) REVERT: F 68 ASP cc_start: 0.9242 (m-30) cc_final: 0.8962 (m-30) REVERT: G 35 ARG cc_start: 0.8225 (mtp-110) cc_final: 0.7943 (mtm110) REVERT: G 36 LYS cc_start: 0.8679 (pttp) cc_final: 0.8227 (mmmt) REVERT: G 38 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8391 (m110) REVERT: H 39 TYR cc_start: 0.8844 (t80) cc_final: 0.8463 (t80) outliers start: 7 outliers final: 6 residues processed: 127 average time/residue: 0.1517 time to fit residues: 25.6468 Evaluate side-chains 130 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 47 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 72 optimal weight: 10.0000 chunk 86 optimal weight: 30.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.151115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.100427 restraints weight = 17697.196| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.15 r_work: 0.2905 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 13650 Z= 0.201 Angle : 0.619 6.876 19865 Z= 0.353 Chirality : 0.045 0.293 2262 Planarity : 0.005 0.036 1368 Dihedral : 32.254 178.406 4452 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.96 % Allowed : 12.32 % Favored : 86.72 % 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: 2.62 (0.31), residues: 736 helix: 2.64 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -1.05 (0.41), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 83 TYR 0.017 0.002 TYR F 51 PHE 0.012 0.002 PHE A 67 HIS 0.005 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (13650) covalent geometry : angle 0.61910 / 0.35 (19865) hydrogen bonds : bond 0.05958 / 4.04 ( 700) hydrogen bonds : angle 3.04850 / 2.22 ( 1796) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3329.86 seconds wall clock time: 57 minutes 41.07 seconds (3461.07 seconds total)